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Yorodumi- PDB-8hgd: Crystal structure of the CYP153A mutant V456A from Marinobacter a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8hgd | ||||||
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Title | Crystal structure of the CYP153A mutant V456A from Marinobacter aquaeolei | ||||||
Components | Cytochrome P450 | ||||||
Keywords | OXIDOREDUCTASE / CYP153A | ||||||
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 | Marinobacter nauticus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 Å | ||||||
Authors | Jiang, Y. / Cong, Z. | ||||||
Funding support | China, 1items
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Citation | Journal: To Be Published Title: Crystal structure of the CYP153A mutant V456A from Marinobacter aquaeolei Authors: Jiang, Y. / Cong, Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8hgd.cif.gz | 115.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8hgd.ent.gz | 82 KB | Display | PDB format |
PDBx/mmJSON format | 8hgd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hg/8hgd ftp://data.pdbj.org/pub/pdb/validation_reports/hg/8hgd | HTTPS FTP |
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-Related structure data
Related structure data | 5fygS 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
#1: Protein | Mass: 55250.988 Da / Num. of mol.: 1 / Mutation: V456A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Marinobacter nauticus (bacteria) / Gene: DET51_1164 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A368UNN3 |
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#2: Chemical | ChemComp-HEM / |
#3: Chemical | ChemComp-MOH / |
#4: Chemical | ChemComp-GOL / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 38.68 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.2 M (NH4)2SO4, 0.1 M HEPES 7.0, 26% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 14, 2022 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.53→50 Å / Num. obs: 65017 / % possible obs: 99.3 % / Redundancy: 3.2 % / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.041 / Rpim(I) all: 0.026 / Rrim(I) all: 0.049 / Χ2: 0.932 / Net I/σ(I): 23.2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5FYG Resolution: 1.53→31.38 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 17.87 / 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: 1.53→31.38 Å
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Refine LS restraints |
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LS refinement shell |
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