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Yorodumi- PDB-6oox: The crystal structure of 4-isopropylbenzoate bound to T252A mutan... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6oox | ||||||
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Title | The crystal structure of 4-isopropylbenzoate bound to T252A mutant of 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: 1.774 Å | ||||||
Authors | Coleman, T. / Bruning, J.B. / Bell, S.G. | ||||||
Funding support | Australia, 1items
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Citation | Journal: To Be Published Title: Structural investigation of the interplay between the substrate and the acid-alcohol pair of residues in cytochrome P450 enzymes 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 | 6oox.cif.gz | 98.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6oox.ent.gz | 71.5 KB | Display | PDB format |
PDBx/mmJSON format | 6oox.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6oox_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 6oox_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6oox_validation.xml.gz | 18.3 KB | Display | |
Data in CIF | 6oox_validation.cif.gz | 25.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oo/6oox ftp://data.pdbj.org/pub/pdb/validation_reports/oo/6oox | HTTPS FTP |
-Related structure data
Related structure data | 6oowC 4do1S 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: 42868.633 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-4IA / |
#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: 1.86 Å3/Da / Density % sol: 33.92 % |
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Crystal grow | Temperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 5.25 Details: 0.1 M Bis-Tris, pH 5.25, 23% w/v PEG3350, 0.2 M magnesium acetate tetrahydrate PH range: 5.0-5.75 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å | ||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 25, 2017 | ||||||||||||||||||||||||||||||
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.77→42.93 Å / Num. obs: 30504 / % possible obs: 99.2 % / Redundancy: 7.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.033 / Rrim(I) all: 0.092 / Net I/σ(I): 12.2 / Num. measured all: 226398 / Scaling rejects: 4 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-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: PDB entry 4DO1 Resolution: 1.774→39.306 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 35.28
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 83.56 Å2 / Biso mean: 32.3008 Å2 / Biso min: 14.75 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.774→39.306 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11
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