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Yorodumi- PDB-2zui: Crystal Structure of Camphor-soaked Ferric Cytochrome P450cam Mut... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2zui | ||||||
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Title | Crystal Structure of Camphor-soaked Ferric Cytochrome P450cam Mutant (D297N) | ||||||
Components | Camphor 5-monooxygenase | ||||||
Keywords | OXIDOREDUCTASE / P450CAM / MONOOXYGENASE / CAMPHOR-HYDROXYLASE / Heme / Iron / Metal-binding / Cytoplasm | ||||||
Function / homology | Function and homology information camphor 5-monooxygenase / camphor 5-monooxygenase activity / (+)-camphor catabolic process / cholest-4-en-3-one 26-monooxygenase activity / steroid hydroxylase activity / cholesterol catabolic process / iron ion binding / heme binding / cytoplasm Similarity search - Function | ||||||
Biological species | Pseudomonas putida (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Sakurai, K. / Harada, K. / Shimada, H. / Shimokata, K. / Hayashi, T. / Tsukihara, T. | ||||||
Citation | Journal: TO BE PUBLISHED Title: Crystal Structure of Camphor-soaked Ferric Cytochrome P450cam Mutant Authors: Sakurai, K. / Harada, K. / Shimada, H. / Shimokata, K. / Hayashi, T. / Tsukihara, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2zui.cif.gz | 123.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zui.ent.gz | 92.4 KB | Display | PDB format |
PDBx/mmJSON format | 2zui.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2zui_validation.pdf.gz | 811.3 KB | Display | wwPDB validaton report |
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Full document | 2zui_full_validation.pdf.gz | 814 KB | Display | |
Data in XML | 2zui_validation.xml.gz | 26 KB | Display | |
Data in CIF | 2zui_validation.cif.gz | 42.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zu/2zui ftp://data.pdbj.org/pub/pdb/validation_reports/zu/2zui | HTTPS FTP |
-Related structure data
Related structure data | 2zuhC 2zujC 2zaxS S: Starting model for refinement C: citing same article (ref.) |
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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: 46719.090 Da / Num. of mol.: 1 / Mutation: D297N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas putida (bacteria) / Strain: cyp101 / Gene: camc / Plasmid: M13tv19 / Production host: Escherichia coli (E. coli) / Strain (production host): Jm109 / References: UniProt: P00183, camphor 5-monooxygenase |
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#2: Chemical | ChemComp-HEM / |
#3: Chemical | ChemComp-CAM / |
#4: Chemical | ChemComp-K / |
#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: 2.71 Å3/Da / Density % sol: 54.56 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.4 Details: 12-15% PEG 4000, 50mM Tris-HCl, 250mM KCl, 1mM d-Camphor, 10mM dithioerythritol(DTE), pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 2, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→33.45 Å / Num. obs: 80010 / % possible obs: 95.7 % / Redundancy: 7 % / Biso Wilson estimate: 15.22 Å2 / Rsym value: 0.042 / Net I/σ(I): 20.3 / Num. measured all: 557635 |
Reflection shell | Resolution: 1.5→1.55 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.185 / Num. unique all: 5908 / % possible all: 72.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2ZAX Resolution: 1.5→33.45 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.963 / SU B: 0.993 / SU ML: 0.038 / Cross valid method: THROUGHOUT / ESU R: 0.067 / ESU R Free: 0.066 / 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: 17.706 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→33.45 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.539 Å / Total num. of bins used: 20
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