+Open data
-Basic information
Entry | Database: PDB / ID: 1j9b | ||||||
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Title | ARSENATE REDUCTASE+0.4M ARSENITE FROM E. COLI | ||||||
Components | ARSENATE REDUCTASE | ||||||
Keywords | OXIDOREDUCTASE / ARSC / REDUCTASE / ARSENITE / ARSENATE | ||||||
Function / homology | Function and homology information arsenate reductase (glutathione/glutaredoxin) / arsenate reductase (glutaredoxin) activity / response to arsenic-containing substance Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.26 Å | ||||||
Authors | Martin, P. / Edwards, B.F. | ||||||
Citation | Journal: Structure / Year: 2001 Title: Insights into the structure, solvation, and mechanism of ArsC arsenate reductase, a novel arsenic detoxification enzyme. Authors: Martin, P. / DeMel, S. / Shi, J. / Gladysheva, T. / Gatti, D.L. / Rosen, B.P. / Edwards, B.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1j9b.cif.gz | 87.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1j9b.ent.gz | 65.3 KB | Display | PDB format |
PDBx/mmJSON format | 1j9b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1j9b_validation.pdf.gz | 436.4 KB | Display | wwPDB validaton report |
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Full document | 1j9b_full_validation.pdf.gz | 438.7 KB | Display | |
Data in XML | 1j9b_validation.xml.gz | 11.9 KB | Display | |
Data in CIF | 1j9b_validation.cif.gz | 17.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j9/1j9b ftp://data.pdbj.org/pub/pdb/validation_reports/j9/1j9b | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 15940.161 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Plasmid: R773 / References: UniProt: P08692 | ||||||||
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#2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Has protein modification | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3 Å3/Da / Density % sol: 68.94 % | ||||||||||||||||||||||||||||
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Crystal grow | Temperature: 278 K / Method: vapor diffusion, hanging drop / pH: 4.8 Details: CESIUM SULFATE, ACETATE, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 278K | ||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 5 ℃ | ||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 93 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 / Wavelength: 1 Å | |||||||||
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jan 20, 2000 | |||||||||
Radiation | Monochromator: Si(111) double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 1.26→20 Å / Num. all: 70105 / Num. obs: 55804 / % possible obs: 79.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 12.155 Å2 / Rmerge(I) obs: 0.059 / Rsym value: 0.059 / Net I/σ(I): 23.6 | |||||||||
Reflection shell | Resolution: 1.26→1.33 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.684 / Mean I/σ(I) obs: 1.4 / Num. unique all: 11094 / Rsym value: 0.684 / % possible all: 34.4 | |||||||||
Reflection | *PLUS Num. obs: 51735 / % possible obs: 90.1 % / Num. measured all: 363771 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: NATIVE STRUCTURE Resolution: 1.26→20 Å / Num. parameters: 13220 / Num. restraintsaints: 15398 / Cross valid method: FREE R / σ(F): 0 / σ(I): 4 / Stereochemistry target values: ENGH AND HUBER Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 1.93%
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Solvent computation | Solvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228 | |||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.098 Å / Num. disordered residues: 9 / Occupancy sum hydrogen: 1110.55 / Occupancy sum non hydrogen: 1398.83 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.26→20 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 5.3 % / Rfactor all: 0.14 / Rfactor obs: 0.128 / Rfactor Rfree: 0.166 / Rfactor Rwork: 0.146 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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