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Yorodumi- PDB-1jfv: X-Ray Structure of oxidised C10S, C15A arsenate reductase from pI258 -
+Open data
-Basic information
Entry | Database: PDB / ID: 1jfv | ||||||
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Title | X-Ray Structure of oxidised C10S, C15A arsenate reductase from pI258 | ||||||
Components | arsenate reductase | ||||||
Keywords | OXIDOREDUCTASE / oxidised / arsenate reductase / perchlorate / potassium | ||||||
Function / homology | Function and homology information arsenate reductase (thioredoxin) / arsenate reductase (thioredoxin) activity / response to arsenic-containing substance / protein tyrosine phosphatase activity / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å | ||||||
Authors | Zegers, I. / Martins, J.C. / Willem, R. / Wyns, L. / Messens, J. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 2001 Title: Arsenate reductase from S. aureus plasmid pI258 is a phosphatase drafted for redox duty. Authors: Zegers, I. / Martins, J.C. / Willem, R. / Wyns, L. / Messens, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jfv.cif.gz | 38 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jfv.ent.gz | 28.8 KB | Display | PDB format |
PDBx/mmJSON format | 1jfv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jf/1jfv ftp://data.pdbj.org/pub/pdb/validation_reports/jf/1jfv | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 14877.399 Da / Num. of mol.: 1 / Mutation: C10S,C15A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: arsC / Plasmid: pTrc99A / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: P0A006 |
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#2: Chemical | ChemComp-LCP / |
#3: Chemical | ChemComp-K / |
#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: 2.22 Å3/Da / Density % sol: 44.49 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: Peg4000, arsenite, sodium perchlorate, potassium chloride, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8 | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 1.043, 1.0425, 0.9918 | ||||||||||||
Detector | Type: MARRESEARCH / Detector: AREA DETECTOR / Date: Jan 1, 2000 | ||||||||||||
Radiation | Monochromator: double crystal focussing monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2→30 Å / Num. all: 9502 / Num. obs: 9502 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 34 % / Biso Wilson estimate: 21.05 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 47 | ||||||||||||
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 30 % / Rmerge(I) obs: 0.361 / % possible all: 100 | ||||||||||||
Reflection | *PLUS Lowest resolution: 30 Å / Num. measured all: 162849 / Rmerge(I) obs: 0.086 | ||||||||||||
Reflection shell | *PLUS % possible obs: 100 % / Rmerge(I) obs: 0.352 / Mean I/σ(I) obs: 7.6 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2→17 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2→17 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.07 Å
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Software | *PLUS Name: CNS / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 5.3 % / Rfactor obs: 0.226 / Rfactor Rfree: 0.271 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: c_angle_deg / Dev ideal: 1.86 |