+Open data
-Basic information
Entry | Database: PDB / ID: 2ve3 | ||||||
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Title | Retinoic acid bound cyanobacterial CYP120A1 | ||||||
Components | PUTATIVE CYTOCHROME P450 120 | ||||||
Keywords | OXIDOREDUCTASE / MONOOXYGENASE / METAL-BINDING / HEME / IRON | ||||||
Function / homology | Function and homology information Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen / sterol metabolic process / 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 | SYNECHOCYSTIS SP. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Kuhnel, K. / Ke, N. / Sligar, S.G. / Schuler, M.A. / Schlichting, I. | ||||||
Citation | Journal: Biochemistry / Year: 2008 Title: Crystal Structures of Substrate-Free and Retinoic Acid-Bound Cyanobacterial Cytochrome P450 Cyp120A1. Authors: Kuhnel, K. / Ke, N. / Cryle, M.J. / Sligar, S.G. / Schuler, M.A. / Schlichting, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ve3.cif.gz | 182.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ve3.ent.gz | 151.9 KB | Display | PDB format |
PDBx/mmJSON format | 2ve3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ve/2ve3 ftp://data.pdbj.org/pub/pdb/validation_reports/ve/2ve3 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 50633.129 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SYNECHOCYSTIS SP. (bacteria) / Strain: PCC 6803 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 (DE3) References: UniProt: Q59990, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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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: 2.89 Å3/Da / Density % sol: 57.4 % / Description: NONE |
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Crystal grow | pH: 6.5 / Details: 1.2 M SODIUM POTASSIUM TARTATE, 0.1 M MES PH6.5 |
-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.0007 |
Detector | Type: MARRESEARCH / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0007 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→20 Å / Num. obs: 62855 / % possible obs: 95 % / Observed criterion σ(I): 3 / Redundancy: 2.9 % / Biso Wilson estimate: 32.6 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 9.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: SUBSTRATE-FREE CYP120A1 Resolution: 2.1→19.85 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.888 / SU B: 6.289 / SU ML: 0.167 / Cross valid method: THROUGHOUT / ESU R: 0.227 / ESU R Free: 0.197 / 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: 27.95 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→19.85 Å
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Refine LS restraints |
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