+Open data
-Basic information
Entry | Database: PDB / ID: 3icr | ||||||
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Title | Crystal structure of oxidized Bacillus anthracis CoADR-RHD | ||||||
Components | Coenzyme A-Disulfide Reductase | ||||||
Keywords | OXIDOREDUCTASE / Pyridine nucleotide-disulfide oxidoreductase class I / Rhodanese / Coenzyme A / Flavin Adenine Dinucleotide | ||||||
Function / homology | Function and homology information CoA-disulfide reductase (NADPH) activity / protein disulfide isomerase activity / NADP binding / flavin adenine dinucleotide binding Similarity search - Function | ||||||
Biological species | Bacillus anthracis (anthrax bacterium) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Wallen, J.R. / Claiborne, A. | ||||||
Citation | Journal: Biochemistry / Year: 2009 Title: Crystal structure and catalytic properties of Bacillus anthracis CoADR-RHD: implications for flavin-linked sulfur trafficking. Authors: Wallen, J.R. / Mallett, T.C. / Boles, W. / Parsonage, D. / Furdui, C.M. / Karplus, P.A. / Claiborne, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3icr.cif.gz | 246.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3icr.ent.gz | 196.2 KB | Display | PDB format |
PDBx/mmJSON format | 3icr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ic/3icr ftp://data.pdbj.org/pub/pdb/validation_reports/ic/3icr | 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: 66008.312 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Ames / Gene: BA0774, BAS0736, BA_0774, GBAA_0774 / Plasmid: pTHCm / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q81UT5, UniProt: A0A6L7H7X4*PLUS #2: Chemical | #3: Chemical | #4: 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: 2.21 Å3/Da / Density % sol: 44.38 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 8-16% PEG 8000, 2% 2-methyl-2,4-pentanediol, 0.2M potassium acetate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 288K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU SATURN 92 / Detector: CCD / Details: Confocal Blue Max-Flux |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→42.56 Å / Num. all: 66890 / Num. obs: 66422 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.097 / Net I/σ(I): 33.6 |
Reflection shell | Resolution: 2.1→2.154 Å / Rmerge(I) obs: 0.302 / Mean I/σ(I) obs: 7.5 / Num. unique all: 61873 / % possible all: 92.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3 wavelength MAD structure deteremined on Selenomethionine-containing CoADR-RHD Resolution: 2.1→42.56 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.926 / SU B: 8.74 / SU ML: 0.126 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.229 / ESU R Free: 0.182 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.417 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→42.56 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.154 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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