+Open data
-Basic information
Entry | Database: PDB / ID: 5h1z | ||||||
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Title | CYP153D17 from Sphingomonas sp. PAMC 26605 | ||||||
Components | putative CYP alkane hydroxylase CYP153D17 | ||||||
Keywords | HYDROLASE / P450 / Alkane Hydroxylase / CYP153D17 / Sphingomonas sp. PAMC 26605 | ||||||
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 | Sphingomonas sp. PAMC 26605 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å | ||||||
Authors | Lee, C.W. / Lee, J.H. | ||||||
Citation | Journal: Int J Mol Sci / Year: 2016 Title: Crystal Structure of a Putative Cytochrome P450 Alkane Hydroxylase (CYP153D17) from Sphingomonas sp. PAMC 26605 and Its Conformational Substrate Binding Authors: Lee, C.W. / Yu, S.C. / Lee, J.H. / Park, S.H. / Park, H. / Oh, T.J. / Lee, J.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5h1z.cif.gz | 96.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5h1z.ent.gz | 73.1 KB | Display | PDB format |
PDBx/mmJSON format | 5h1z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h1/5h1z ftp://data.pdbj.org/pub/pdb/validation_reports/h1/5h1z | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 46825.379 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sphingomonas sp. PAMC 26605 (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1S4NYE0*PLUS |
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#2: Chemical | ChemComp-HEM / |
#3: Chemical | ChemComp-D12 / |
#4: Water | ChemComp-HOH / |
Sequence details | THE SEQUENCE HAS BEEN DEPOSITED TO NCBI WITH ACCESSION CODE WP_010183267.1 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.38 Å3/Da / Density % sol: 71.9 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 23% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97933 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 2, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97933 Å / Relative weight: 1 |
Reflection | Resolution: 3.08→95.99 Å / Num. obs: 14358 / % possible obs: 91.3 % / Redundancy: 4.5 % / Net I/σ(I): 26.76 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→50.01 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.829 / SU B: 27.911 / SU ML: 0.451 / Cross valid method: THROUGHOUT / ESU R Free: 0.551 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 97.778 Å2
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Refinement step | Cycle: 1 / Resolution: 3.1→50.01 Å
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