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Yorodumi- PDB-3bpk: Crystal structure of nitrilotriacetate monooxygenase component B ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3bpk | ||||||
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Title | Crystal structure of nitrilotriacetate monooxygenase component B from Bacillus cereus | ||||||
Components | Nitrilotriacetate monooxygenase component B | ||||||
Keywords | OXIDOREDUCTASE / structural genomics / APC25244 / nitrilotriacetate monooxygenase / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | Function and homology information Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With NADH or NADPH as one donor, and incorporation of one atom of oxygen into the other donor / monooxygenase activity / FMN binding Similarity search - Function | ||||||
Biological species | Bacillus cereus ATCC 14579 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.56 Å | ||||||
Authors | Osipiuk, J. / Quartey, P. / Abdullah, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: X-ray crystal structure of nitrilotriacetate monooxygenase component B from Bacillus cereus. Authors: Osipiuk, J. / Quartey, P. / Abdullah, J. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3bpk.cif.gz | 197.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3bpk.ent.gz | 166.6 KB | Display | PDB format |
PDBx/mmJSON format | 3bpk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3bpk_validation.pdf.gz | 451.7 KB | Display | wwPDB validaton report |
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Full document | 3bpk_full_validation.pdf.gz | 457.5 KB | Display | |
Data in XML | 3bpk_validation.xml.gz | 23.3 KB | Display | |
Data in CIF | 3bpk_validation.cif.gz | 35.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bp/3bpk ftp://data.pdbj.org/pub/pdb/validation_reports/bp/3bpk | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | AUTHORS STATE THAT THE DIMERIC ASSEMBLY OF THE BIOLOGICAL UNIT THAT IS SHOWN IN REMARK 350 IS PUTATIVE AT THE TIME OF DEPOSITION. |
-Components
#1: Protein | Mass: 22618.400 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus cereus ATCC 14579 (bacteria) / Species: Bacillus cereus / Strain: DSM 31 / Gene: BC_5322 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: Q814U7, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With NADH or NADPH as one donor, and incorporation of one atom of oxygen into the other donor #2: Chemical | ChemComp-CL / #3: Chemical | ChemComp-SO4 / | #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: 2.78 Å3/Da / Density % sol: 55.82 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 2 M Ammonium sulfate, 0.1 M Cacodylate buffer, 0.2 M Sodium chloride, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 16, 2005 |
Radiation | Monochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.56→39.7 Å / Num. all: 72506 / Num. obs: 72506 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.4 % / Biso Wilson estimate: 30.7 Å2 / Rmerge(I) obs: 0.066 / Χ2: 1.313 / Net I/σ(I): 18.3 |
Reflection shell | Resolution: 1.56→1.6 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.512 / Mean I/σ(I) obs: 2.26 / Num. unique all: 4984 / Χ2: 0.848 / % possible all: 95.2 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.56→39.7 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.964 / SU B: 2.642 / SU ML: 0.044 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.086 / ESU R Free: 0.072 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.797 Å2
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Refinement step | Cycle: LAST / Resolution: 1.56→39.7 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.56→1.6 Å / Total num. of bins used: 20
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