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Yorodumi- PDB-7n60: The crystal structure of 4-methoxybenzoate-bound CYP199A S244D mutant -
+Open data
-Basic information
Entry | Database: PDB / ID: 7n60 | ||||||
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Title | The crystal structure of 4-methoxybenzoate-bound CYP199A S244D mutant | ||||||
Components | Cytochrome P450 | ||||||
Keywords | OXIDOREDUCTASE / P450 | ||||||
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: 1.892 Å | ||||||
Authors | Lau, I.C.K. / Coleman, T. / Bell, S.G. / Bruning, J.B. | ||||||
Funding support | Australia, 1items
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Citation | Journal: To Be Published Title: The crystal structure of 4-methoxybenzoate-bound CYP199A S244D mutant Authors: Lau, I.C.K. / Coleman, T. / Bell, S.G. / Bruning, J.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7n60.cif.gz | 109.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7n60.ent.gz | 78.3 KB | Display | PDB format |
PDBx/mmJSON format | 7n60.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7n60_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 7n60_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 7n60_validation.xml.gz | 22.7 KB | Display | |
Data in CIF | 7n60_validation.cif.gz | 35.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n6/7n60 ftp://data.pdbj.org/pub/pdb/validation_reports/n6/7n60 | HTTPS FTP |
-Related structure data
Related structure data | 4do1S S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 42926.668 Da / Num. of mol.: 1 / Fragment: UNP residues 18-410 / Mutation: S244D 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, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen |
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-Non-polymers , 5 types, 570 molecules
#2: Chemical | ChemComp-HEM / |
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#3: Chemical | ChemComp-ANN / |
#4: Chemical | ChemComp-MG / |
#5: Chemical | ChemComp-CL / |
#6: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
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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: 1.95 Å3/Da / Density % sol: 36.9 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.25 Details: 0.1 M Bis-Tris, pH 5.25, 22% PEG3350, 0.2 M magnesium acetate |
-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: Apr 19, 2016 | |||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 1.89→43 Å / Num. obs: 25827 / % possible obs: 96.1 % / Redundancy: 6.2 % / Biso Wilson estimate: 12.73 Å2 / CC1/2: 0.975 / Rmerge(I) obs: 0.304 / Rpim(I) all: 0.13 / Rrim(I) all: 0.331 / Net I/σ(I): 5.7 / Num. measured all: 160287 / Scaling rejects: 398 | |||||||||||||||||||||
Reflection shell |
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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: 1.892→42.998 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.36
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 57.78 Å2 / Biso mean: 13.8643 Å2 / Biso min: 2.35 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.892→42.998 Å
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Refine LS restraints |
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LS refinement shell |
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