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Yorodumi- PDB-3cgc: Pyridine Nucleotide Complexes with Bacillus anthracis Coenzyme A-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3cgc | ||||||
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Title | Pyridine Nucleotide Complexes with Bacillus anthracis Coenzyme A-Disulfide Reductase: A Structural Analysis of Dual NAD(P)H Specificity | ||||||
Components | Pyridine nucleotide-disulfide oxidoreductase, class I | ||||||
Keywords | OXIDOREDUCTASE / coenzyme A / flavin adenine dinucleotide / FAD / Flavoprotein | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Bacillus anthracis str. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Wallen, J.R. | ||||||
Citation | Journal: Biochemistry / Year: 2008 Title: Pyridine Nucleotide Complexes with Bacillus anthracis Coenzyme A-Disulfide Reductase: A Structural Analysis of Dual NAD(P)H Specificity. Authors: Wallen, J.R. / Paige, C. / Mallett, T.C. / 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 | 3cgc.cif.gz | 198 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3cgc.ent.gz | 157 KB | Display | PDB format |
PDBx/mmJSON format | 3cgc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3cgc_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 3cgc_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 3cgc_validation.xml.gz | 37.8 KB | Display | |
Data in CIF | 3cgc_validation.cif.gz | 53.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cg/3cgc ftp://data.pdbj.org/pub/pdb/validation_reports/cg/3cgc | HTTPS FTP |
-Related structure data
Related structure data | 3cgbSC 3cgdC 3cgeC S: Starting model for refinement C: citing same article (ref.) |
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Similar 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: 53577.832 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus anthracis str. (bacteria) / Species: Bacillus anthracis / Strain: Ames / Gene: pyridine nucleotide-disulfide oxidoreductase, class I / Plasmid: pTrcHisC / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q81TK8, UniProt: A0A6L7HMK7*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: 3.09 Å3/Da / Density % sol: 60.14 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 16-26% 2-methyl-2,4-pentanediol, 0.2 M magnesium acetate, 0.1 M sodium cacodylate, pH 6.5, and 2 mM NAD(P)+, 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 / Date: Sep 29, 2005 / 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: 2.3→25.61 Å / Num. all: 58130 / Num. obs: 58072 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 19.8 |
Reflection shell | Resolution: 2.3→2.42 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.279 / Mean I/σ(I) obs: 6 / Num. unique all: 8452 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3CGB Resolution: 2.3→25.11 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.901 / SU B: 5.619 / SU ML: 0.139 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.25 / ESU R Free: 0.207 / 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: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.1 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→25.11 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.359 Å / Total num. of bins used: 20
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