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Yorodumi- PDB-2afc: X-Ray Crystal Structure of Protein Q8A8B0 from Bacteroides thetai... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2afc | ||||||
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Title | X-Ray Crystal Structure of Protein Q8A8B0 from Bacteroides thetaiotaomicron. Northeast Structural Genomics Consortium Target BtR9. | ||||||
Components | conserved hypothetical protein | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / Q8A8B0 BtR9 NESG X-Ray / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Bacteroides thetaiotaomicron (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å | ||||||
Authors | Kuzin, A.P. / Abashidze, M. / Vorobiev, S.M. / Acton, T. / Xiao, R. / Conover, K. / Ma, L.-C. / Cunninggham, K.E. / Montelione, G.T. / Hunt, J.F. ...Kuzin, A.P. / Abashidze, M. / Vorobiev, S.M. / Acton, T. / Xiao, R. / Conover, K. / Ma, L.-C. / Cunninggham, K.E. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: To be Published Title: X-ray structure of Q8A8B0 hypothetical protein from Bacteroides thetaiotaomicron Authors: Kuzin, A.P. / Abashidze, M. / Vorobiev, S.M. / Acton, T. / Xiao, R. / Conover, K. / Ma, L.-C. / Cunninggham, K.E. / Montelione, G.T. / Hunt, J.F. / Tong, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2afc.cif.gz | 70.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2afc.ent.gz | 56.9 KB | Display | PDB format |
PDBx/mmJSON format | 2afc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2afc_validation.pdf.gz | 413.3 KB | Display | wwPDB validaton report |
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Full document | 2afc_full_validation.pdf.gz | 419.6 KB | Display | |
Data in XML | 2afc_validation.xml.gz | 9.1 KB | Display | |
Data in CIF | 2afc_validation.cif.gz | 13.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/af/2afc ftp://data.pdbj.org/pub/pdb/validation_reports/af/2afc | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 19233.412 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria) Gene: BT1257 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL31(DE3) + Magic / References: UniProt: Q8A8B0 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 39 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.1 Details: 35% PEG3350, 0.1M MES, pH 7.1, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97908 / Wavelength: 0.97908 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 15, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97908 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→30 Å / Num. all: 18721 / % possible obs: 92.4 % / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Biso Wilson estimate: 16 Å2 / Rsym value: 0.036 / Net I/σ(I): 36.3 |
Reflection shell | Resolution: 2.5→2.59 Å / Mean I/σ(I) obs: 25.5 / Rsym value: 0.046 / % possible all: 96.5 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.5→27.61 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 493404.85 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 29.2547 Å2 / ksol: 0.342812 e/Å3 | ||||||||||||||||||||
Displacement parameters | Biso mean: 20 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→27.61 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
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Xplor file |
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