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Yorodumi- PDB-4py9: Crystal structure of an exopolyphosphatase-related protein from B... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4py9 | |||||||||
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Title | Crystal structure of an exopolyphosphatase-related protein from Bacteroides Fragilis. Northeast Structural Genomics target BFR192 | |||||||||
Components | Putative exopolyphosphatase-related protein | |||||||||
Keywords | UNKNOWN FUNCTION / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / EXOPOLYPHOSPHATASE-RELATED PROTEIN | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Bacteroides fragilis (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.25 Å | |||||||||
Authors | Seetharaman, J. / Abashidze, M. / Wang, H. / Janjua, H. / Foote, E.L. / Xiao, R. / Nair, R. / Everett, J.K. / Acton, T.B. / Rost, B. ...Seetharaman, J. / Abashidze, M. / Wang, H. / Janjua, H. / Foote, E.L. / Xiao, R. / Nair, R. / Everett, J.K. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG) | |||||||||
Citation | Journal: To be Published Title: Crystal structure of an exopolyphosphatase-related protein from Bacteroides Fragilis. Northeast Structural Genomics target BFR192 Authors: Seetharaman, J. / Abashidze, M. / Wang, H. / Janjua, H. / Foote, E.L. / Xiao, R. / Nair, R. / Everett, J.K. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast ...Authors: Seetharaman, J. / Abashidze, M. / Wang, H. / Janjua, H. / Foote, E.L. / Xiao, R. / Nair, R. / Everett, J.K. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG) | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4py9.cif.gz | 79.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4py9.ent.gz | 64.2 KB | Display | PDB format |
PDBx/mmJSON format | 4py9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4py9_validation.pdf.gz | 440.6 KB | Display | wwPDB validaton report |
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Full document | 4py9_full_validation.pdf.gz | 441.6 KB | Display | |
Data in XML | 4py9_validation.xml.gz | 14.8 KB | Display | |
Data in CIF | 4py9_validation.cif.gz | 20.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/py/4py9 ftp://data.pdbj.org/pub/pdb/validation_reports/py/4py9 | 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: 39771.703 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides fragilis (bacteria) / Gene: BF3900 / Plasmid: PET 21 / Production host: Escherichia coli (E. coli) / References: UniProt: Q64PD9 | ||||
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#2: Chemical | ChemComp-PO4 / #3: Chemical | ChemComp-NA / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.23 Å3/Da / Density % sol: 61.9 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 320 MM KACETATE, 100 MM NAACETATE, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 4r / Detector: CCD / Date: Jun 4, 2008 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→50 Å / Num. all: 47146 / Num. obs: 40928 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.5 % / Rmerge(I) obs: 0.074 / Rsym value: 0.056 / Net I/σ(I): 17.3 |
Reflection shell | Resolution: 2.25→2.33 Å / Redundancy: 11.4 % / Rmerge(I) obs: 0.432 / Mean I/σ(I) obs: 17 / Rsym value: 0.28 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.25→45.45 Å / SU B: 6.366 / SU ML: 0.157 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.312 / ESU R Free: 0.236 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.288 Å2
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Refinement step | Cycle: LAST / Resolution: 2.25→45.45 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.252→2.31 Å / Total num. of bins used: 20
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