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- PDB-2oed: GB3 solution structure obtained by refinement of X-ray structure ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2oed | ||||||
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Title | GB3 solution structure obtained by refinement of X-ray structure with dipolar couplings | ||||||
![]() | Immunoglobulin G-binding protein G | ||||||
![]() | IMMUNE SYSTEM / residual dipolar couplings | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
![]() | Ulmer, T.S. / Ramirez, B.E. / Delaglio, F. / Bax, A. / Grishaev, A. | ||||||
![]() | ![]() Title: Evaluation of backbone proton positions and dynamics in a small protein by liquid crystal NMR spectroscopy Authors: Ulmer, T.S. / Ramirez, B.E. / Delaglio, F. / Bax, A. #1: ![]() Title: The third IGG-binding domain from Streptococcal protein G. An analysis by X-ray crystallography of the structure alone and in a complex with FAB Authors: Derrick, J.P. / Wiggley, D.B. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 27 KB | Display | ![]() |
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PDB format | ![]() | 17.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 240.9 KB | Display | ![]() |
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Full document | ![]() | 240.6 KB | Display | |
Data in XML | ![]() | 2.2 KB | Display | |
Data in CIF | ![]() | 2.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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NMR ensembles |
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Components
#1: Antibody | Mass: 6214.848 Da / Num. of mol.: 1 / Fragment: THIRD IGG-BINDING DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||
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NMR experiment |
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Sample preparation
Details | Contents: 25 MM NAH2PO4/NA2HPO4, 0.2 MG/ML NAN3, 1.5 MM GB3 PROTEIN AND ALIGNING MEDIA, 90% H2O, 10% D2O Solvent system: 90% H2O/10% D2O |
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Sample conditions | Ionic strength: 0.05 / pH: 6.5 / Pressure: ambient / Temperature: 300 K |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M | |||||||||||||||
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Radiation wavelength | Relative weight: 1 | |||||||||||||||
NMR spectrometer |
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Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 Details: GB3 solution structure is obtained by refinement of the x-ray structure of gb3 (1igd) with c(alpha)-c', c'-n, c(alpha)-h(alpha) and N-H dipolar couplings measured in five aligning media ...Details: GB3 solution structure is obtained by refinement of the x-ray structure of gb3 (1igd) with c(alpha)-c', c'-n, c(alpha)-h(alpha) and N-H dipolar couplings measured in five aligning media (bicelle, peg, pf1 phage, negatively and positively charged polyacrylamide gels). Dipolar couplings originating on residues 10-11, 24-26, 39-41 and the n- and c-terminal residues were excluded, resulting in near-identity with the x-ray structure for these residues. This deposition corresponds to the refined-II structure of the primary citation that was refined against all 4 types of dipolar couplings in 5 media. The related depositions 1P7E and 1P7F correspond to the refined-III and refined-IV structures, respectively. The deposited structure was calculated with DYNAMO 2.1 following a short low-temperature molecular dynamics simulated annealing run starting from the regularized coordinates of the X-ray structure 1IGD using atomic coordinate restraints to the overlapping 3-residue segments of 1IGD. The force constants for the HN-N-C-Ca impropers were softened 10-fold relative to their standard settings. See the primary citation and the corresponding supporting information file for a detailed description of the refinement procedure. The deposited restraints file includes, in addition to the dipolar couplings and backbone H-bond distance restraints (XPLOR/CNS format), an Xplor-NIH script designed to mimic the deposited structure, and the force field parameter files. A set of overlapping 3-residue NCS restraint terms is used in this script in place of the Dynamo atomic coordinate restraints. | ||||||||||||
NMR representative | Selection criteria: best agreement with dipolar restraints | ||||||||||||
NMR ensemble | Conformer selection criteria: all calculated structures submitted Conformers calculated total number: 1 / Conformers submitted total number: 1 |