+Open data
-Basic information
Entry | Database: PDB / ID: 6c3h | ||||||
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Title | The crystal structure of 4-n-heptylbenzoate-bound CYP199A4 | ||||||
Components | Cytochrome P450 | ||||||
Keywords | OXIDOREDUCTASE / P450 / Substrate | ||||||
Function / homology | Function and homology information cholest-4-en-3-one 26-monooxygenase activity / steroid hydroxylase activity / cholesterol catabolic process / iron ion binding / heme binding Similarity search - Function | ||||||
Biological species | Rhodopseudomonas palustris (phototrophic) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.705 Å | ||||||
Authors | Coleman, T. / Bruning, J.B. / Bell, S.G. | ||||||
Funding support | Australia, 1items
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Citation | Journal: To Be Published Title: The crystal structure of 4-n-heptylbenzoate-bound CYP199A4 Authors: Coleman, T. / Bruning, J.B. / Bell, S.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6c3h.cif.gz | 107.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6c3h.ent.gz | 76.6 KB | Display | PDB format |
PDBx/mmJSON format | 6c3h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6c3h_validation.pdf.gz | 815.9 KB | Display | wwPDB validaton report |
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Full document | 6c3h_full_validation.pdf.gz | 819 KB | Display | |
Data in XML | 6c3h_validation.xml.gz | 21.5 KB | Display | |
Data in CIF | 6c3h_validation.cif.gz | 33.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c3/6c3h ftp://data.pdbj.org/pub/pdb/validation_reports/c3/6c3h | HTTPS FTP |
-Related structure data
Related structure data | 5kdbS 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: 42898.660 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodopseudomonas palustris (strain HaA2) (phototrophic) Strain: HaA2 / Gene: RPB_3613 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2IU02 |
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#2: Chemical | ChemComp-HEM / |
#3: Chemical | ChemComp-EJV / |
#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: 2.09 Å3/Da / Density % sol: 41.23 % |
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Crystal grow | Temperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: McAc, 0.2M Bis-Tris, 0.1M, pH 5.5 PEG-3350, 26 % w/v PH range: 5.25-6.0 / Temp details: 16 C |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Apr 19, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.705→44.491 Å / Num. obs: 38417 / % possible obs: 99.4 % / Redundancy: 4.1 % / Biso Wilson estimate: 18.32 Å2 / Rmerge(I) obs: 0.142 / Rpim(I) all: 0.082 / Net I/σ(I): 19.7 |
Reflection shell | Resolution: 1.705→1.7506 Å / Rmerge(I) obs: 0.777 / Rpim(I) all: 0.482 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5KDB Resolution: 1.705→44.491 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.28
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 81.33 Å2 / Biso mean: 22.5525 Å2 / Biso min: 11.01 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.705→44.491 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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