+Open data
-Basic information
Entry | Database: PDB / ID: 4dnj | ||||||
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Title | The crystal structures of 4-methoxybenzoate bound CYP199A2 | ||||||
Components | Putative cytochrome P450 | ||||||
Keywords | OXIDOREDUCTASE | ||||||
Function / homology | Function and homology information 4-methoxybenzoate monooxygenase (O-demethylating) / 4-methoxybenzoate monooxygenase (O-demethylating) activity / xenobiotic metabolic process / iron ion binding / heme binding / cytoplasm Similarity search - Function | ||||||
Biological species | Rhodopseudomonas palustris (phototrophic) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Zhou, W. / Bell, S.G. / Yang, W. / Tan, A.B.H. / Zhou, R. / Johnson, E.O.D. / Zhang, A. / Rao, Z. / Wong, L.-L. | ||||||
Citation | Journal: Dalton Trans / Year: 2012 Title: The crystal structures of 4-methoxybenzoate bound CYP199A2 and CYP199A4: structural changes on substrate binding and the identification of an anion binding site Authors: Bell, S.G. / Yang, W. / Tan, A.B.H. / Zhou, R. / Johnson, E.O.D. / Zhang, A. / Zhou, W. / Rao, Z. / Wong, L.-L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4dnj.cif.gz | 105.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4dnj.ent.gz | 77.8 KB | Display | PDB format |
PDBx/mmJSON format | 4dnj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dn/4dnj ftp://data.pdbj.org/pub/pdb/validation_reports/dn/4dnj | HTTPS FTP |
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-Related structure data
Related structure data | 4dnzC 4do1C 2rf7S 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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Unit cell |
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-Components
#1: Protein | Mass: 44672.625 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodopseudomonas palustris (phototrophic) Strain: CGA009 / Gene: RPA1871 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q6N8N2, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen |
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#2: Chemical | ChemComp-HEM / |
#3: Chemical | ChemComp-ANN / |
#4: Chemical | ChemComp-CL / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 43.05 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.4 Details: 0.1M Tris, 26% PEG 4000, 10% isopropanol, pH 8.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-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 RAXIS HTC / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. all: 36699 / Num. obs: 36209 / % possible obs: 98.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5 % / Biso Wilson estimate: 15.577 Å2 / Rmerge(I) obs: 0.077 / Rsym value: 0.063 / Net I/σ(I): 25.2 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.264 / Mean I/σ(I) obs: 6.64 / Num. unique all: 3521 / Rsym value: 0.248 / % possible all: 97.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2RF7 Resolution: 1.8→29.07 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.936 / SU B: 2.342 / SU ML: 0.074 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.128 / ESU R Free: 0.125 / 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: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.577 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→29.07 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.799→1.846 Å / Rfactor Rfree error: 0.125 / Total num. of bins used: 20
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