+Open data
-Basic information
Entry | Database: PDB / ID: 4fyz | ||||||
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Title | Crystal Structure of Nitrosyl Cytochrome P450cin | ||||||
Components | P450cin1,8-Cineole 2-endo-monooxygenase | ||||||
Keywords | OXIDOREDUCTASE / P450 / HEME / MONOOXYGENASE / CINDOXIN | ||||||
Function / homology | Function and homology information 1,8-cineole 2-endo-monooxygenase / carbazole catabolic process / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen / iron ion binding / heme binding Similarity search - Function | ||||||
Biological species | Citrobacter braakii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.32 Å | ||||||
Authors | Madrona, Y. / Tripathi, S.M. / Li, H. / Poulos, T.L. | ||||||
Citation | Journal: Biochemistry / Year: 2012 Title: Crystal structures of substrate-free and nitrosyl cytochrome p450cin: implications for o(2) activation. Authors: Madrona, Y. / Tripathi, S. / Li, H. / Poulos, T.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4fyz.cif.gz | 178.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4fyz.ent.gz | 140.5 KB | Display | PDB format |
PDBx/mmJSON format | 4fyz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fy/4fyz ftp://data.pdbj.org/pub/pdb/validation_reports/fy/4fyz | HTTPS FTP |
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-Related structure data
Related structure data | 4fb2C 4fmxC 4g3rC 1t2bS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 44787.879 Da / Num. of mol.: 2 / Fragment: UNP residues 8-404 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Citrobacter braakii (bacteria) / Gene: CIN A, cinA / Plasmid: pcWori-P450cin / Production host: Escherichia coli (E. coli) / Strain (production host): DH5-alpha / References: UniProt: Q8VQF6 |
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-Non-polymers , 6 types, 336 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | #7: 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: 2.54 Å3/Da / Density % sol: 51.53 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.2 Details: 6-9% PEG 3350, 100mM Bis-Tris pH 6.2, 100mM Lithium Sulfate, 5mM Cineole, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 70 K | |||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å | |||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Jan 1, 2002 | |||||||||||||||||||||||||||||||||
Radiation | Monochromator: Cu Filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.32→50 Å / Num. all: 37894 / Num. obs: 37894 / % possible obs: 97.1 % / Observed criterion σ(F): 0.02 / Observed criterion σ(I): -3 / Redundancy: 5 % / Biso Wilson estimate: 30.1 Å2 / Rsym value: 0.071 / Net I/σ(I): 19.8 | |||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: P450cin wild-type (PDB ID:1T2B) Resolution: 2.32→36.013 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.15 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.618 Å2 / ksol: 0.363 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.32→36.013 Å
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Refine LS restraints |
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LS refinement shell |
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