NMR paper Joint refinement as a tool for thorough comparison between NMR and X-ray data and str

		BioNMR > Educational resources > Journal club
[NMR paper] Joint refinement as a tool for thorough comparison between NMR and X-ray data and str

Webservers

NMR processing:

MDD

NMR assignment:

Backbone:

Side-chains:

NOEs:

Structure from NMR restraints:

Ab initio:

Fragment-based:

Rosetta-NMR (Robetta)

Template-based:

GeNMR

I-TASSER

Refinement:

Amber

Structure from chemical shifts:

Fragment-based:

Homology-based:

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:

NMR model quality:

NOEs, other restraints:

Chemical shifts:

RDCs:

Pseudocontact shifts:

Protein geomtery:

SAVES2 or SAVES4

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:

Isotope labeling:

Solid-state NMR:

Thread Tools

Search this Thread

Rate Thread

Display Modes

11-19-2010, 08:44 PM

nmrlearner

Senior Member

Join Date: Jan 2005

Posts: 23,777

Points: 193,617, Level: 100

Level up: 0%, 0 Points needed

Activity: 50.7%

Last Achievements

Award-Showcase

NMR Credits: 0

NMR Points: 193,617

Downloads: 0

Uploads: 0

Joint refinement as a tool for thorough comparison between NMR and X-ray data and str

Joint refinement as a tool for thorough comparison between NMR and X-ray data and structures of HU protein.

Related Articles Joint refinement as a tool for thorough comparison between NMR and X-ray data and structures of HU protein.

J Biomol NMR. 2001 Nov;21(3):235-48

Authors: Raves ML, Doreleijer JF, Vis H, Vorgias CE, Wilson KS, Kaptei R

Joint refinement, i.e., the simultaneous refinement of a structure against both nuclear magnetic resonance (NMR) spectroscopic and X-ray crystallographic data, was performed on the HU protein from Bacillus stearothermophilus (HUBst). The procedure was aimed at investigating the compatibility of the two data sets and at identifying conflicting information. Wherever important differences were found, such as peptide flips in the main-chain conformation, the data were further analyzed to find the cause. The NMR data showed some errors arising either from the manual interpretation of the spectra or from the incorrect account for spin diffusion. The most important artefact inherent to the X-ray data is the crystal packing of the molecules: the effects range from the limitation of the freedom of the flexible parts of the HUBst molecule to possibly one of the peptide flips.

PMID: 11775740 [PubMed - indexed for MEDLINE]

Source: PubMed

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
High-resolution membrane protein structure by joint calculations with solid-state NMR and X-ray experimental data High-resolution membrane protein structure by joint calculations with solid-state NMR and X-ray experimental data Abstract X-ray diffraction and nuclear magnetic resonance spectroscopy (NMR) are the staple methods for revealing atomic structures of proteins. Since crystals of biomolecular assemblies and membrane proteins often diffract weakly and such large systems encroach upon the molecular tumbling limit of solution NMR, new methods are essential to extend structures of such systems to high resolution. Here we present a method that incorporates solid-state NMR restraints alongside...	nmrlearner	Journal club	0	09-26-2011 06:42 AM
High-resolution membrane protein structure by joint calculations with solid-state NMR and X-ray experimental data. High-resolution membrane protein structure by joint calculations with solid-state NMR and X-ray experimental data. High-resolution membrane protein structure by joint calculations with solid-state NMR and X-ray experimental data. J Biomol NMR. 2011 Sep 22; Authors: Tang M, Sperling LJ, Berthold DA, Schwieters CD, Nesbitt AE, Nieuwkoop AJ, Gennis RB, Rienstra CM Abstract X-ray diffraction and nuclear magnetic resonance spectroscopy (NMR) are the staple methods for revealing atomic structures of proteins. Since crystals of biomolecular...	nmrlearner	Journal club	0	09-23-2011 05:30 PM
[NMR paper] Joint X-ray and NMR refinement of the yeast L30e-mRNA complex. Joint X-ray and NMR refinement of the yeast L30e-mRNA complex. Related Articles Joint X-ray and NMR refinement of the yeast L30e-mRNA complex. Structure. 2004 Jul;12(7):1165-76 Authors: Chao JA, Williamson JR L30e, a Saccharomyces cervisiae ribosomal protein, regulates its own expression by binding to a purine-rich asymmetric internal loop located in both its pre-mRNA and mature mRNA. A crystal structure of an MBP-L30e fusion protein in complex with an RNA containing the pre-mRNA regulatory site was solved at 3.24 A. Interestingly, the...	nmrlearner	Journal club	0	11-24-2010 09:51 PM
[NMR paper] Structure refinement of the glucocorticoid receptor-DNA binding domain from NMR data Structure refinement of the glucocorticoid receptor-DNA binding domain from NMR data by relaxation matrix calculations. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Structure refinement of the glucocorticoid receptor-DNA binding domain from NMR data by relaxation matrix calculations. J Mol Biol. 1995 Apr 7;247(4):689-700 Authors: van Tilborg MA, Bonvin AM, Hård K, Davis AL, Maler B, Boelens R, Yamamoto KR, Kaptein R The solution structure of the glucocorticoid...	nmrlearner	Journal club	0	08-22-2010 03:41 AM
[NMR paper] A systematic comparison of three structure determination methods from NMR data: depen A systematic comparison of three structure determination methods from NMR data: dependence upon quality and quantity of data. Related Articles A systematic comparison of three structure determination methods from NMR data: dependence upon quality and quantity of data. J Biomol NMR. 1992 Jul;2(4):373-88 Authors: Liu Y, Zhao D, Altman R, Jardetzky O We have systematically examined how the quality of NMR protein structures depends on (1) the number of NOE distance constraints, (2) their assumed precision, (3) the method of structure calculation...	nmrlearner	Journal club	0	08-21-2010 11:41 PM
[NMR paper] Motional effects on NMR structural data. Comparison of spinach and Escherichia coli a Motional effects on NMR structural data. Comparison of spinach and Escherichia coli acyl carrier proteins. Related Articles Motional effects on NMR structural data. Comparison of spinach and Escherichia coli acyl carrier proteins. Biochem Pharmacol. 1990 Jul 1;40(1):7-13 Authors: Kim Y, Ohlrogge JB, Prestegard JH Proteins in solution need not exist in a single rigid structure but can exist in a dynamic equilibrium among structural forms. The problems that this poses for structure determination using nuclear Overhauser effect data from...	nmrlearner	Journal club	0	08-21-2010 10:48 PM
[NMR paper] Refinement of the NMR structures for acyl carrier protein with scalar coupling data. Refinement of the NMR structures for acyl carrier protein with scalar coupling data. Related Articles Refinement of the NMR structures for acyl carrier protein with scalar coupling data. Proteins. 1990;8(4):377-85 Authors: Kim Y, Prestegard JH Structure determination of small proteins using NMR data is most commonly pursued by combining NOE derived distance constraints with inherent constraints based on chemical bonding. Ideally, one would make use of a variety of experimental observations, not just distance constraints. Here, coupling...	nmrlearner	Journal club	0	08-21-2010 10:48 PM
[NMR paper] A branch and bound algorithm for protein structure refinement from sparse NMR data se A branch and bound algorithm for protein structure refinement from sparse NMR data sets. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles A branch and bound algorithm for protein structure refinement from sparse NMR data sets. J Mol Biol. 1999 Jan 29;285(4):1691-710 Authors: Standley DM, Eyrich VA, Felts AK, Friesner RA, McDermott AE We describe new methods for predicting protein tertiary structures to low resolution given the specification of secondary structure and a...	nmrlearner	Journal club	0	08-21-2010 04:03 PM

« Previous Thread | Next Thread »

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