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Yorodumi- PDB-8vkf: The crystal structure of wild-type CYP199A4 bound to 4-propionylb... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8vkf | ||||||
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Title | The crystal structure of wild-type CYP199A4 bound to 4-propionylbenzoic acid | ||||||
Components | Cytochrome P450 | ||||||
Keywords | OXIDOREDUCTASE / Cytochrome P450 / CYP199A4 | ||||||
Function / homology | Function and homology information oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity / iron ion binding / heme binding Similarity search - Function | ||||||
Biological species | Rhodopseudomonas palustris HaA2 (phototrophic) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Podgorski, M.N. / Bell, S.G. | ||||||
Funding support | Australia, 1items
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Citation | Journal: To Be Published Title: The crystal structure of wild-type CYP199A4 bound to 4-propionylbenzoic acid Authors: Podgorski, M.N. / 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 | 8vkf.cif.gz | 105.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8vkf.ent.gz | 75.9 KB | Display | PDB format |
PDBx/mmJSON format | 8vkf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vk/8vkf ftp://data.pdbj.org/pub/pdb/validation_reports/vk/8vkf | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-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: 44587.430 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodopseudomonas palustris HaA2 (phototrophic) Gene: RPB_3613 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q2IU02 |
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-Non-polymers , 5 types, 458 molecules
#2: Chemical | ChemComp-HEM / |
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#3: Chemical | ChemComp-LVK / Mass: 178.185 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H10O3 / Feature type: SUBJECT OF INVESTIGATION |
#4: Chemical | ChemComp-CL / |
#5: Chemical | ChemComp-MG / |
#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: 1.86 Å3/Da / Density % sol: 33.98 % |
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Crystal grow | Temperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: The crystallization buffer was 100 mM Bis-Tris buffer (adjusted to pH 5.0-5.75 with acetic acid), 0.2 M magnesium acetate and 20-32% PEG 3350 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: 0.95372 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 12, 2020 |
Radiation | Monochromator: Double-crystal Si(111) water-cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95372 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→43.04 Å / Num. obs: 36229 / % possible obs: 99.8 % / Redundancy: 6.5 % / CC1/2: 0.995 / Rmerge(I) obs: 0.173 / Rpim(I) all: 0.074 / Rrim(I) all: 0.189 / Χ2: 0.95 / Net I/σ(I): 7.4 / Num. measured all: 234344 |
Reflection shell | Resolution: 1.7→1.73 Å / % possible obs: 99.6 % / Redundancy: 6.6 % / Rmerge(I) obs: 1.638 / Num. measured all: 12545 / Num. unique obs: 1906 / CC1/2: 0.67 / Rpim(I) all: 0.689 / Rrim(I) all: 1.781 / Χ2: 0.76 / Net I/σ(I) obs: 1.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→40.913 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.3 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→40.913 Å
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Refine LS restraints |
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LS refinement shell |
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