Re: [ccp4bb] Judging a homology model
Dear Friends, I have a question about judging a homology model. I have three homologous proteins A, B and C of which only A has 3D crystal structure available. Their similarities/identities are given below. Pair-wise alignment similarity/identity (%) A and B 63/49 A and C 54/39 B and C 60/46 Assuming all the above data are right, which of the following way would give the best model for C? 1. Building homology model of C with A as template. 2.Building homology model of B with A as template and then use B as template to build C. Suppose I used MODELLER for this work where an energy minimization step is involved after threading the query sequence on the template. I need to know which model for C will be better and why? Thanks for your answer… Happy New Year to you all, Raja Raja, you should take the alignment of B to A into account when you establish the alignment of C to A. In other words, construct a multiple alignment first (and use sequences D, E, ... as well if they exist), and only then build your homology model. The reason is that the biggest source of error in a homology model comes from misalignment of the target and the model sequence. You want to avoid this. HTH, Kay smime.p7s Description: S/MIME Cryptographic Signature
[ccp4bb] Lots of noise in structure
Dear All, Happy New Year I am working with a 2.06 Ang resolution structure in F432 space group and further using REFMAC (also tried Phenix) program for refinement of my model. Every thing in the structure seems good, R factor/ R free= 18.59/20.77 but the structure is too noisy (blobs of difference Fourier with red as well as green density). As such electron density is looking good for the protein part. Is there any parameter which i had to check. Thanking you in advance Rajan -- Current Address: Rajan Vyas Research Scholar Deptt. of Biotechnology Panjab University Chandigarh, India 160014Mob. +919417374197 Fax: +91-172-2625254
[ccp4bb] Anions in protein structures
Dear CCP4ers Can anyone recommend their favourite paper, or review, that discusses anions in protein structures. Thanks in advance and Happy New Year Gina Notice: This e-mail message, together with any attachments, contains information of Merck & Co., Inc. (One Merck Drive, Whitehouse Station, New Jersey, USA 08889), and/or its affiliates Direct contact information for affiliates is available at http://www.merck.com/contact/contacts.html) that may be confidential, proprietary copyrighted and/or legally privileged. It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system.
Re: [ccp4bb] Judging a homology model
Hi Raja, 1) how big is your protein ? 2) multiple domains ? What's the ID/sim between domains ? 3) Check Xtalpred in case you've overlooked a closer homolog http://ffas.burnham.org/XtalPred-cgi/xtal.pl I would not try to predict an intermediate model and then use that to predict the final model. Jürgen On Jan 5, 2010, at 12:24 PM, Raja Dey wrote: Dear Friends, I have a question about judging a homology model. I have three homologous proteins A, B and C of which only A has 3D crystal structure available. Their similarities/identities are given below. Pair-wise alignment similarity/identity (%) A and B 63/49 A and C 54/39 B and C 60/46 Assuming all the above data are right, which of the following way would give the best model for C? 1. Building homology model of C with A as template. 2.Building homology model of B with A as template and then use B as template to build C. Suppose I used MODELLER for this work where an energy minimization step is involved after threading the query sequence on the template. I need to know which model for C will be better and why? Thanks for your answer… Happy New Year to you all, Raja The INTERNET now has a personality. YOURS! See your Yahoo! Homepage. - Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry & Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Phone: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-3655 http://web.mac.com/bosch_lab/
Re: [ccp4bb] Judging a homology model
On Tue, Jan 5, 2010 at 9:24 AM, Raja Dey wrote: > Assuming all the above data are right, which of the following way would > give the best model for C? > > 1. Building homology model of C with A as template. > > 2.Building homology model of B with A as template and then use B as > template to build C. > > Suppose I used MODELLER for this work where an energy minimization step is > involved after threading the query sequence on the template. > > I need to know which model for C will be better and why? > (1). I don't have time to list all of the reasons, but it is a certainty that the dissimilar residues between A and B are not all in the same positions as the dissimilar residues in B and C, and each dissimilar residue is going to result in a less accurate model - so if you model A->B->C, you will be propagating errors. (There is probably a formal mathematical way to express this - there have been many studies on sequence similarity vs. RMSD.) If you need to convince yourself further, find three structures with similar sequence identities in the PDB, run the experiment with them, and compare the end result to the actual structures.
[ccp4bb] Judging a homology model
Dear Friends, I have a question about judging a homology model. I have three homologous proteins A, B and C of which only A has 3D crystal structure available. Their similarities/identities are given below. Pair-wise alignment similarity/identity (%) A and B 63/49 A and C 54/39 B and C 60/46 Assuming all the above data are right, which of the following way would give the best model for C? 1. Building homology model of C with A as template. 2.Building homology model of B with A as template and then use B as template to build C. Suppose I used MODELLER for this work where an energy minimization step is involved after threading the query sequence on the template. I need to know which model for C will be better and why? Thanks for your answer… Happy New Year to you all, Raja The INTERNET now has a personality. YOURS! See your Yahoo! Homepage. http://in.yahoo.com/
Re: [ccp4bb] PDB Validation Report
Dear Katja, You can find below information from PDB Format Guide, http://www.wwpdb.org/documentation/format32/remarks2.html#REMARK%20500. The improper CA-C-CB-N angles for chiral centers are calculated and are listed in REMARK 500 of PDB file. It is defined below with 10 degree allowed deviations. +35 for L amino acids -35 for D amino acids * +25 to +45 degree range is defined as sp3, L. If D is expected, it gives "WRONG HAND" in the details. If the calculated value is positive and outside this range, it gives "OUTSIDE RANGE" in the details. * -10 to +10 degree range is defined as sp2, planar. If it is expected to be sp2 and the value is outside this range, it gives "EXPECTING PLANAR" in the details. If it is expected to be sp3 and the value is within this range, it gives "EXPECTING SP3" in the details. * -45 to -25 degree range is defined as sp3, D. If L is expected, it gives "WRONG HAND" in the details. If the calculated value is negative and outside this range, it gives "OUTSIDE RANGE" in the details. Hope this information help. Jasmine From: Katja Schleider To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] PDB Validation Report Dear all, I just finished my first protein structure. More or less. I'm using right now the pdb validation server to check the data and the data look quite well. The only point irretating is following line in the Adit Validation Report: The following residues have unexpected configuration of the chiral center using C(i) - N(i) - Ca(i) - Cb(i) chirality. Residue Chain Sequence Improper Details LYS A 470 22.18 Expecting L Found L OUTSIDE RANGE I am not sure what this means and what I should do. What is outside the L range? I would be thankful for any advice. Thanks, Katja -- === Jasmine Young, Ph.D. RCSB Protein Data Bank Assistant Research Professor Lead biocurator Department of Chemistry and Chemical Biology Rutgers The State University of New Jersey 610 Taylor Road Piscataway, NJ 08854-8087 Email:+jas...@rcsb.rutgers.edu Phone:+(732)445-0103+ext 231 Fax: (732)445-4320 ===
[ccp4bb] refmac problem
Hello again I am refine my model using TLS and restrained refinement, and I got below the error message from refmac although the program claim to be successful. There is no output mtz and pdb files. Any suggestions are appreciated! Many thanks! Jane ***TLS refinement cycle***7 1 0.26529309 0.40231493 0.31580201 -5.07818013E-02 0.17374255 -0.39783996 2.04001069E-02 7.82079645E-04 1.11576570E-04 -3.76230048E-04 -2.82397377E-04 -1.06552179E-04 4.59514521E-02 -2.79289447E-02 -1.72524340E-02 -1.04173245E-02 -1.80899426E-02 -7.60819018E-03 8.42294842E-03 1.78668604E-04 -2.46240292E-02 Problem xyz 6193 -16.111391 -2.8551121 -5.0709343 -4.46808338E-03 0.43998715 0.84659839 0.22162700 -0.42724574 0.15069498 -0.42246437 -4.46808338E-03 0.21654272 1.2961377 0.22026606 0.85707664 -0.46572798 imac4:~ jbailey$ ccp4i Top level CCP4 directory is /sw/share/xtal/ccp4-6.1.2 Using CCP4 programs from /sw/share/xtal/ccp4-6.1.2/bin 15:03:39 MoveFile: input file /tmp/jbailey/native_580_24_2_pdb_1.tmp does not exis t 15:03:39 MoveFile: input file /tmp/jbailey/native_580_24_3_mtz_1.tmp does not exis t 15:03:39 MoveFile: input file /tmp/jbailey/native_580_24_4_tls_1.tmp does not exis t
[ccp4bb] refmac problem
Hello again I am refine my model using TLS and restrained refinement, and I got below the error message from refmac although the program claim to be successful. There is no output mtz and pdb files. Any suggestions are appreciated! Many thanks! Jane ***TLS refinement cycle***7 1 0.26529309 0.40231493 0.31580201 -5.07818013E-02 0.17374255 -0.39783996 2.04001069E-02 7.82079645E-04 1.11576570E-04 -3.76230048E-04 -2.82397377E-04 -1.06552179E-04 4.59514521E-02 -2.79289447E-02 -1.72524340E-02 -1.04173245E-02 -1.80899426E-02 -7.60819018E-03 8.42294842E-03 1.78668604E-04 -2.46240292E-02 Problem xyz 6193 -16.111391 -2.8551121 -5.0709343 -4.46808338E-03 0.43998715 0.84659839 0.22162700 -0.42724574 0.15069498 -0.42246437 -4.46808338E-03 0.21654272 1.2961377 0.22026606 0.85707664 -0.46572798 imac4:~ jbailey$ ccp4i Top level CCP4 directory is /sw/share/xtal/ccp4-6.1.2 Using CCP4 programs from /sw/share/xtal/ccp4-6.1.2/bin 15:03:39 MoveFile: input file /tmp/jbailey/native_580_24_2_pdb_1.tmp does not exis t 15:03:39 MoveFile: input file /tmp/jbailey/native_580_24_3_mtz_1.tmp does not exis t 15:03:39 MoveFile: input file /tmp/jbailey/native_580_24_4_tls_1.tmp does not exis t
Re: [ccp4bb] xds process gave different cell parameters
Hi I think that even post-refining with high resolution data you are unlikely to refine reliably to the same value within 1 part in 10,000 if you are making small differences to your processing. The differences you have are what I would consider to be within experimental error, so I wouldn't worry about them at all. > Hi > > I was processing my data with XDS several runs, they gave slightly > different cell parameters everytime, eg: > 1) 77.100 103.850 116.550 90.00 90.00 90.00 P 21 21 21 > 2) 77.086 103.821 116.533 90.00 90.00 90.00 P 21 21 21 > > I have already a refined model from 1), can I use this model to > refine against dataset 2) by simply change the cell parameter in the > pdb file? There's nothing wrong with dataset 1), just wonder whether it > is doable . > > Many thanks > Jane >
Re: [ccp4bb] xds process gave different cell parameters
Nothing wrong with that approach in principle. You may want to have a few cycles of rigid body refinement before classical refinement. Just in case (but the cell parameters are very very close indeed). And the starting Rfactors should tell you if there is a problem or not. Fred. Jane Bailey wrote: Hi I was processing my data with XDS several runs, they gave slightly different cell parameters everytime, eg: 1) 77.100 103.850 116.550 90.00 90.00 90.00 P 21 21 21 2) 77.086 103.821 116.533 90.00 90.00 90.00 P 21 21 21 I have already a refined model from 1), can I use this model to refine against dataset 2) by simply change the cell parameter in the pdb file? There's nothing wrong with dataset 1), just wonder whether it is doable . Many thanks Jane
[ccp4bb] xds process gave different cell parameters
Hi I was processing my data with XDS several runs, they gave slightly different cell parameters everytime, eg: 1) 77.100 103.850 116.550 90.00 90.00 90.00 P 21 21 21 2) 77.086 103.821 116.533 90.00 90.00 90.00 P 21 21 21 I have already a refined model from 1), can I use this model to refine against dataset 2) by simply change the cell parameter in the pdb file? There's nothing wrong with dataset 1), just wonder whether it is doable . Many thanks Jane
[ccp4bb] PhD position at Structural Biology Brussels, Belgium
PHD POSITION IN STRUCTURAL BIOLOGY - STRUCTURAL BIOLOGY BRUSSELS (VUB/VIB), BRUSSELS, BELGIUM We are looking for a highly motivated PhD student interested in biochemical and structural studies on tRNA modifying enzymes and enzyme complexes at The Structural Biology Brussels laboratory (Vrije Universiteit Brussel / VIB) – Brussels, Belgium. VIB (the Flanders Institute for Biotechnology) is an interdisciplinary non-profit research institute based at 4 Flemish universities and employs a vibrant community of 1000 life scientists. The Structural Biology Brussels lab focuses on the functioning of proteins in all its aspects. Our multidisciplinary team of about 40 researchers is housed in new laboratory facilities and combines extensive expertise in structural biology (X-ray crystallography, NMR and atomic force microscopy), biophysics and molecular biology (for more info: http://www.structuralbiology.be/). Project description: One of the topics in our lab deals with the study of the structure and function of tRNA modifying enzymes. tRNA molecules are transcribed as precursors that need to be extensively processed and chemically modified before they can be used in translation. Many bases in tRNA undergo post-transcriptional modification to increase the stability, to modify cognate codon recognition and to affect aminoacylation properties. Many of these post-transcriptional modifications are critical for proper tRNA function. During your PhD you will be studying the functioning of tRNA modifying enzyme complexes and the interaction with their tRNA substrates, using an integrated approach of X-ray crystallography, enzyme kinetics and different biophysical methods. Start date: The position is available immediately and will remain vacant until a suitable candidate is found. Profile: Candidates should have a recent Masters degree in Biochemistry, Bio- engineering, Biology, Chemistry or related. Skills in either molecular biology or protein chemistry & purification or protein crystallography would be an asset. Contact: Please send applications (including CV, research experience, and at least two names and contact information for references) to: Wim Versées, Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussel, Belgium - wim.vers...@vub.ac.be. --- Wim Versées Structural Biology Brussels, Vrije Universiteit Brussel VIB Department of Molecular and Cellular Interactions Vrije Universiteit Brussel Pleinlaan 2, 1050 Brussel, Belgium phone: +32 2 6291849 fax: +32 2 6291963 e-mail: wim.vers...@vub.ac.be
