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Yorodumi- PDB-5kdz: The crystal structure of the T252A mutant of CYP199A4 in complex ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5kdz | ||||||
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Title | The crystal structure of the T252A mutant of CYP199A4 in complex with 4-methoxybenzoate | ||||||
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: 1.424 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 the T252A mutant of CYP199A4 in complex with 4-methoxybenzoate 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 | 5kdz.cif.gz | 180.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5kdz.ent.gz | 136.6 KB | Display | PDB format |
PDBx/mmJSON format | 5kdz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kd/5kdz ftp://data.pdbj.org/pub/pdb/validation_reports/kd/5kdz | HTTPS FTP |
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-Related structure data
Related structure data | 4do1S 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: 42868.633 Da / Num. of mol.: 1 / Mutation: T253A 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-ANN / |
#3: Chemical | ChemComp-HEM / |
#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: 1.96 Å3/Da / Density % sol: 37.33 % |
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Crystal grow | Temperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 5.25 Details: 0.2M Magnesium acetate PEG 3350, 23% w/v 0.1M Bis-Tris, pH 5.25 PH range: 5.25 - 6 / Temp details: 16 degrees C |
-Data collection
Diffraction | Mean temperature: 100 K |
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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: Aug 10, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 1.424→79.45 Å / Num. obs: 62253 / % possible obs: 95.9 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 13 |
Reflection shell | Resolution: 1.424→1.45 Å / Redundancy: 4.1 % / % possible all: 79.9 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB: 4DO1 Resolution: 1.424→25.308 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 16.11
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 72.76 Å2 / Biso mean: 10.6767 Å2 / Biso min: 1.41 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.424→25.308 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18
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