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- PDB-2ra8: Crystal structure of the Q64V53_BACFR protein from Bacteroides fr... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2ra8 | ||||||
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Title | Crystal structure of the Q64V53_BACFR protein from Bacteroides fragilis. Northeast Structural Genomics Consortium target BfR43 | ||||||
![]() | Uncharacterized protein Q64V53_BACFR | ||||||
![]() | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / Q64V53 / WGR DOMAIN / LRR DOMAIN / LEUCINE RICH REPEATS / BFR43 / NESG / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium | ||||||
Function / homology | ![]() WGR domain / q64v53_bacfr protein fold / WGR domain / WGR domain superfamily / WGR domain / Proposed nucleic acid binding domain / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / Single Sheet ...WGR domain / q64v53_bacfr protein fold / WGR domain / WGR domain superfamily / WGR domain / Proposed nucleic acid binding domain / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / Single Sheet / Leucine-rich repeat domain superfamily / Mainly Beta / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Vorobiev, S.M. / Abashidze, M. / Seetharaman, J. / Wang, D. / Cunningham, K. / Maglaqui, M. / Owens, L. / Xiao, R. / Acton, T.B. / Montelione, G.T. ...Vorobiev, S.M. / Abashidze, M. / Seetharaman, J. / Wang, D. / Cunningham, K. / Maglaqui, M. / Owens, L. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG) | ||||||
![]() | ![]() Title: Crystal structure of the Q64V53_BACFR protein from Bacteroides fragilis. Authors: Vorobiev, S.M. / Abashidze, M. / Seetharaman, J. / Wang, D. / Cunningham, K. / Maglaqui, M. / Owens, L. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 83.7 KB | Display | ![]() |
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PDB format | ![]() | 67 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 433.8 KB | Display | ![]() |
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Full document | ![]() | 438.1 KB | Display | |
Data in XML | ![]() | 16.9 KB | Display | |
Data in CIF | ![]() | 24.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 |
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Unit cell |
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Components on special symmetry positions |
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Details | Dimer according to the aggregation analysis; second part of the biological assembly is generated by -x+1,y,-z+1 symmetry operator. |
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Components
#1: Protein | Mass: 41852.574 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.91 % Description: The structure factor file contains Friedel pairs |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 16-18% PEG 3350, 0.2M Magnesium acetate, 0.1M Cacodylic acid pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 25, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97922 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→50 Å / Num. all: 52396 / Num. obs: 52396 / % possible obs: 94.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.9 % / Biso Wilson estimate: 9.6 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 14.35 |
Reflection shell | Resolution: 1.95→2.02 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.239 / Mean I/σ(I) obs: 2.25 / Num. unique all: 5541 / % possible all: 99.2 |
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Processing
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Refinement | Method to determine structure: ![]() Details: 1. The Friedel pairs were used for phasing. 2. Cys 116 was modified to s-(dimethylarsenic)cysteine by cacodylic buffer. 3. Tyr 316 is located in a generously allowed position on Ramachandran ...Details: 1. The Friedel pairs were used for phasing. 2. Cys 116 was modified to s-(dimethylarsenic)cysteine by cacodylic buffer. 3. Tyr 316 is located in a generously allowed position on Ramachandran plot. However, Tyr 316 electron density is very well defined and could be interpreted unambiguously.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 60.8472 Å2 / ksol: 0.348442 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.95→19.39 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2.07 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
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Xplor file |
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