BioNMR
NMR aggregator & online community since 2003
BioNMR    
Learn or help to learn NMR - get free NMR books!
 

Go Back   BioNMR > Educational resources > Journal club
Advanced Search
Home Forums Wiki NMR feeds Downloads Register Today's Posts



Jobs Groups Conferences Literature Pulse sequences Software forums Programs Sample preps Web resources BioNMR issues


Webservers
NMR processing:
MDD
NMR assignment:
Backbone:
Autoassign
MARS
UNIO Match
PINE
Side-chains:
UNIO ATNOS-Ascan
NOEs:
UNIO ATNOS-Candid
UNIO Candid
ASDP
Structure from NMR restraints:
Ab initio:
GeNMR
Cyana
XPLOR-NIH
ASDP
UNIO ATNOS-Candid
UNIO Candid
Fragment-based:
BMRB CS-Rosetta
Rosetta-NMR (Robetta)
Template-based:
GeNMR
I-TASSER
Refinement:
Amber
Structure from chemical shifts:
Fragment-based:
WeNMR CS-Rosetta
BMRB CS-Rosetta
Homology-based:
CS23D
Simshift
Torsion angles from chemical shifts:
Preditor
TALOS
Promega- Proline
Secondary structure from chemical shifts:
CSI (via RCI server)
TALOS
MICS caps, β-turns
d2D
PECAN
Flexibility from chemical shifts:
RCI
Interactions from chemical shifts:
HADDOCK
Chemical shifts re-referencing:
Shiftcor
UNIO Shiftinspector
LACS
CheckShift
RefDB
NMR model quality:
NOEs, other restraints:
PROSESS
PSVS
RPF scores
iCing
Chemical shifts:
PROSESS
CheShift2
Vasco
iCing
RDCs:
DC
Anisofit
Pseudocontact shifts:
Anisofit
Protein geomtery:
Resolution-by-Proxy
PROSESS
What-If
iCing
PSVS
MolProbity
SAVES2 or SAVES4
Vadar
Prosa
ProQ
MetaMQAPII
PSQS
Eval123D
STAN
Ramachandran Plot
Rampage
ERRAT
Verify_3D
Harmony
Quality Control Check
NMR spectrum prediction:
FANDAS
MestReS
V-NMR
Flexibility from structure:
Backbone S2
Methyl S2
B-factor
Molecular dynamics:
Gromacs
Amber
Antechamber
Chemical shifts prediction:
From structure:
Shiftx2
Sparta+
Camshift
CH3shift- Methyl
ArShift- Aromatic
ShiftS
Proshift
PPM
CheShift-2- Cα
From sequence:
Shifty
Camcoil
Poulsen_rc_CS
Disordered proteins:
MAXOCC
Format conversion & validation:
CCPN
From NMR-STAR 3.1
Validate NMR-STAR 3.1
NMR sample preparation:
Protein disorder:
DisMeta
Protein solubility:
camLILA
ccSOL
Camfold
camGroEL
Zyggregator
Isotope labeling:
UPLABEL
Solid-state NMR:
sedNMR


Reply
 
Thread Tools Search this Thread Rate Thread Display Modes
  #1  
Old 12-01-2010, 06:56 PM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 23,697
Points: 193,617, Level: 100
Points: 193,617, Level: 100 Points: 193,617, Level: 100 Points: 193,617, Level: 100
Level up: 0%, 0 Points needed
Level up: 0% Level up: 0% Level up: 0%
Activity: 50.7%
Activity: 50.7% Activity: 50.7% Activity: 50.7%
Last Achievements
Award-Showcase
NMR Credits: 0
NMR Points: 193,617
Downloads: 0
Uploads: 0
Default Comparison of X-ray and NMR structures: is there a systematic difference in residue contacts between X-ray- and NMR-resolved protein structures?

Comparison of X-ray and NMR structures: is there a systematic difference in residue contacts between X-ray- and NMR-resolved protein structures?

Related Articles Comparison of X-ray and NMR structures: is there a systematic difference in residue contacts between X-ray- and NMR-resolved protein structures?

Proteins. 2005 Jul 1;60(1):139-47

Authors: Garbuzynskiy SO, Melnik BS, Lobanov MY, Finkelstein AV, Galzitskaya OV

We have compared structures of 78 proteins determined by both NMR and X-ray methods. It is shown that X-ray and NMR structures of the same protein have more differences than various X-ray structures obtained for the protein, and even more than various NMR structures of the protein. X-ray and NMR structures of 18 of these 78 proteins have obvious large-scale structural differences that seem to reflect a difference of crystal and solution structures. The other 60 pairs of structures have only small-scale differences comparable with differences between various X-ray or various NMR structures of a protein; we have analyzed these structures more attentively. One of the main differences between NMR and X-ray structures concerns the number of contacts per residue: (1) NMR structures presented in PDB have more contacts than X-ray structures at distances below 3.0 A and 4.5-6.5 A, and fewer contacts at distances of 3.0-4.5 A and 6.5-8.0 A; (2) this difference in the number of contacts is greater for internal residues than for external ones, and it is larger for beta-containing proteins than for all-alpha proteins. Another significant difference is that the main-chain hydrogen bonds identified in X-ray and NMR structures often differ. Their correlation is 69% only. However, analogous difference is found for refined and rerefined NMR structures, allowing us to suggest that the observed difference in interresidue contacts of X-ray and NMR structures of the same proteins is due mainly to a difference in mathematical treatment of experimental results.

PMID: 15856480 [PubMed - indexed for MEDLINE]



Source: PubMed
Reply With Quote


Did you find this post helpful? Yes | No

Reply
Similar Threads
Thread Thread Starter Forum Replies Last Post
Mapping residue-specific contacts of polymyxin B with lipopolysaccharide by saturation transfer difference NMR: insights into outer-membrane disruption and endotoxin neutralization.
Mapping residue-specific contacts of polymyxin B with lipopolysaccharide by saturation transfer difference NMR: insights into outer-membrane disruption and endotoxin neutralization. Mapping residue-specific contacts of polymyxin B with lipopolysaccharide by saturation transfer difference NMR: insights into outer-membrane disruption and endotoxin neutralization. Biopolymers. 2011;96(3):273-87 Authors: Bhunia A, Bhattacharjya S Abstract High-resolution interactions studies of molecules with lipopolysaccharide (LPS) or endotoxin are...
nmrlearner Journal club 0 09-21-2011 03:31 PM
Systematic comparison of crystal and NMR protein structures deposited in the protein data bank.
Systematic comparison of crystal and NMR protein structures deposited in the protein data bank. Systematic comparison of crystal and NMR protein structures deposited in the protein data bank. Open Biochem J. 2010;4:83-95 Authors: Sikic K, Tomic S, Carugo O Nearly all the macromolecular three-dimensional structures deposited in Protein Data Bank were determined by either crystallographic (X-ray) or Nuclear Magnetic Resonance (NMR) spectroscopic methods. This paper reports a systematic comparison of the crystallographic and NMR results deposited in...
nmrlearner Journal club 0 02-05-2011 05:28 PM
[NMR paper] NMR structures of three single-residue variants of the human prion protein.
NMR structures of three single-residue variants of the human prion protein. Related Articles NMR structures of three single-residue variants of the human prion protein. Proc Natl Acad Sci U S A. 2000 Jul 18;97(15):8340-5 Authors: Calzolai L, Lysek DA, Guntert P, von Schroetter C, Riek R, Zahn R, Wüthrich K The NMR structures of three single-amino acid variants of the C-terminal domain of the human prion protein, hPrP(121-230), are presented. In hPrP(M166V) and hPrP(R220K) the substitution is with the corresponding residue in murine PrP, and in...
nmrlearner Journal club 0 11-19-2010 08:29 PM
[NMR paper] Comparison of X-ray and NMR structures for the Antennapedia homeodomain-DNA complex.
Comparison of X-ray and NMR structures for the Antennapedia homeodomain-DNA complex. Related Articles Comparison of X-ray and NMR structures for the Antennapedia homeodomain-DNA complex. Nat Struct Biol. 1998 Aug;5(8):692-7 Authors: Fraenkel E, Pabo CO Homeodomains are one of the key families of eukaryotic DNA-binding motifs and provide an important model system for studying protein-DNA interactions. We have crystallized the Antennapedia homeodomain-DNA complex and solved this structure at 2.4 A resolution. NMR and molecular dynamics studies...
nmrlearner Journal club 0 11-17-2010 11:15 PM
Comparison of NMR and crystal structures for the proteins TM1112 and TM1367.
Comparison of NMR and crystal structures for the proteins TM1112 and TM1367. Related Articles Comparison of NMR and crystal structures for the proteins TM1112 and TM1367. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010 Oct 1;66(Pt 10):1381-92 Authors: Mohanty B, Serrano P, Pedrini B, Jaudzems K, Geralt M, Horst R, Herrmann T, Elsliger MA, Wilson IA, Wüthrich K The NMR structures of the TM1112 and TM1367 proteins from Thermotoga maritima in solution at 298 K were determined following a new protocol which uses the software package UNIO for...
nmrlearner Journal club 0 10-16-2010 03:56 PM
[NMR paper] Comparison of the NMR and X-ray structures of the HIV-1 matrix protein: evidence for
Comparison of the NMR and X-ray structures of the HIV-1 matrix protein: evidence for conformational changes during viral assembly. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www3.interscience.wiley.com-aboutus-images-wiley_interscience_pubmed_logo_FREE_120x27.gif http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www.pubmedcentral.nih.gov-corehtml-pmc-pmcgifs-pubmed-pmc.gif Related Articles Comparison of the NMR and X-ray structures of the HIV-1 matrix protein: evidence for conformational changes during viral assembly. Protein Sci. 1996...
nmrlearner Journal club 0 08-22-2010 02:20 PM
[NMR paper] Comparison of protein structures in solution using local conformations derived from N
Comparison of protein structures in solution using local conformations derived from NMR data: application to cytochrome c. Related Articles Comparison of protein structures in solution using local conformations derived from NMR data: application to cytochrome c. J Biomol Struct Dyn. 1994 Dec;12(3):527-58 Authors: Kar L, Sherman SA, Johnson ME Structural comparisons of proteins in solution are often required to examine structure-functional relationships, study structural effects of mutations or distinguish between various forms of the same...
nmrlearner Journal club 0 08-22-2010 03:29 AM
[NMR paper] Comparison of protein structures determined by NMR in solution and by X-ray diffracti
Comparison of protein structures determined by NMR in solution and by X-ray diffraction in single crystals. Related Articles Comparison of protein structures determined by NMR in solution and by X-ray diffraction in single crystals. Q Rev Biophys. 1992 Aug;25(3):325-77 Authors: Billeter M
nmrlearner Journal club 0 08-21-2010 11:45 PM



Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is On
Trackbacks are Off
Pingbacks are Off
Refbacks are Off



BioNMR advertisements to pay for website hosting and domain registration. Nobody does it for us.



Powered by vBulletin® Version 3.7.3
Copyright ©2000 - 2024, Jelsoft Enterprises Ltd.
Copyright, BioNMR.com, 2003-2013
Search Engine Friendly URLs by vBSEO 3.6.0

All times are GMT. The time now is 11:19 AM.


Map