+Open data
-Basic information
Entry | Database: PDB / ID: 4bnq | ||||||
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Title | The structure of the Staphylococcus aureus Ham1 protein | ||||||
Components | NON-CANONICAL PURINE NTP PYROPHOSPHATASE | ||||||
Keywords | HYDROLASE / HAM / INOSINE TRIPHOSPHATE PYROPHOSPHATASE | ||||||
Function / homology | Function and homology information XTP/dITP diphosphatase / purine nucleoside triphosphate catabolic process / XTP diphosphatase activity / dITP diphosphatase activity / nucleotide metabolic process / ribonucleoside triphosphate phosphatase activity / nucleotide binding / metal ion binding Similarity search - Function | ||||||
Biological species | STAPHYLOCOCCUS AUREUS SUBSP. AUREUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.279 Å | ||||||
Authors | Abergel, C. / Claverie, J.M. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2013 Title: Molecular Replacement: Tricks and Treats. Authors: Abergel, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4bnq.cif.gz | 89 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4bnq.ent.gz | 69.8 KB | Display | PDB format |
PDBx/mmJSON format | 4bnq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4bnq_validation.pdf.gz | 450.5 KB | Display | wwPDB validaton report |
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Full document | 4bnq_full_validation.pdf.gz | 453.7 KB | Display | |
Data in XML | 4bnq_validation.xml.gz | 18 KB | Display | |
Data in CIF | 4bnq_validation.cif.gz | 25.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bn/4bnq ftp://data.pdbj.org/pub/pdb/validation_reports/bn/4bnq | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 21441.094 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) STAPHYLOCOCCUS AUREUS SUBSP. AUREUS (bacteria) Strain: N315 / Plasmid: IN HOUSE / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 References: UniProt: P99094, nucleoside-triphosphate diphosphatase #2: Chemical | ChemComp-PO4 / #3: Chemical | ChemComp-GOL / | #4: Water | ChemComp-HOH / | Sequence details | LACK OF INITIAL MET | |
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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: 3.31 Å3/Da / Density % sol: 63 % / Description: NONE |
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Crystal grow | Details: 20% AMSO4, PH 6 |
-Data collection
Diffraction | Mean temperature: 105 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.97974 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97974 Å / Relative weight: 1 |
Reflection | Resolution: 2.28→43.4 Å / Num. obs: 26528 / % possible obs: 85.7 % / Observed criterion σ(I): 1.34 / Redundancy: 4.1 % / Biso Wilson estimate: 34.8 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 5.8 |
Reflection shell | Resolution: 2.28→2.4 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 3.4 / % possible all: 85.7 |
-Processing
Software |
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Refinement | Method to determine structure: MAD Starting model: NONE Resolution: 2.279→43.398 Å / SU ML: 0.27 / σ(F): 1.34 / Phase error: 25.46 / Stereochemistry target values: ML / Details: THE TWO MONOMERS ADOPT DIFFERENT CONFORMATIONS
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.279→43.398 Å
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Refine LS restraints |
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LS refinement shell |
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