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Yorodumi- PDB-2qbo: Crystal structure of the P450cam G248V mutant in the cyanide boun... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2qbo | ||||||
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Title | Crystal structure of the P450cam G248V mutant in the cyanide bound state | ||||||
Components | Cytochrome P450-cam | ||||||
Keywords | OXIDOREDUCTASE / CYP101 / mutant / conserved active site residue / cyanide complex / Gly248 / heme geometry | ||||||
Function / homology | Function and homology information camphor 5-monooxygenase / camphor 5-monooxygenase activity / (+)-camphor catabolic process / iron ion binding / heme binding / cytoplasm Similarity search - Function | ||||||
Biological species | Pseudomonas putida (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.9 Å | ||||||
Authors | von Koenig, K. / Makris, T.M. / Sligar, S.D. / Schlichting, I. | ||||||
Citation | Journal: Biochemistry / Year: 2007 Title: Alteration of P450 Distal Pocket Solvent Leads to Impaired Proton Delivery and Changes in Heme Geometry. Authors: Makris, T.M. / Koenig, K.V. / Schlichting, I. / Sligar, S.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2qbo.cif.gz | 109.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2qbo.ent.gz | 80.9 KB | Display | PDB format |
PDBx/mmJSON format | 2qbo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qb/2qbo ftp://data.pdbj.org/pub/pdb/validation_reports/qb/2qbo | HTTPS FTP |
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-Related structure data
Related structure data | 2qblC 2qbmC 2qbnC 1yrcS C: citing same article (ref.) S: Starting model for refinement |
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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 on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 47591.023 Da / Num. of mol.: 1 / Mutation: G248V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: camC, cyp101 / Plasmid: pET28 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P00183, camphor 5-monooxygenase |
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-Non-polymers , 5 types, 524 molecules
#2: Chemical | ChemComp-CYN / |
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#3: Chemical | ChemComp-K / |
#4: Chemical | ChemComp-HEM / |
#5: Chemical | ChemComp-CAM / |
#6: 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: 2.57 Å3/Da / Density % sol: 52.1 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.4 Details: 1 UL OF 15 MG/ML P450 IN 50 MM Potassium phosphate, 250 MM KCL WERE MIXED WITH AN EQUAL VOLUME OF THE RESERVOIR SOLUTION (100 mM Tris, 250 mM KCl, 27-30% PEG 8000, 100 MM DTE), pH 7.4, VAPOR ...Details: 1 UL OF 15 MG/ML P450 IN 50 MM Potassium phosphate, 250 MM KCL WERE MIXED WITH AN EQUAL VOLUME OF THE RESERVOIR SOLUTION (100 mM Tris, 250 mM KCl, 27-30% PEG 8000, 100 MM DTE), pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.006 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 12, 2005 / Details: DYNAMICALLY BENDABLE MIRROR |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.006 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→20 Å / Num. all: 39886 / Num. obs: 39886 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Rsym value: 0.049 / Net I/σ(I): 15 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 3.3 / Num. unique all: 5399 / Rsym value: 0.334 / % possible all: 96 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB entry 1yrc Resolution: 1.9→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: maximum likelihood
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Solvent computation | Bsol: 39.019 Å2 | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.067 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→20 Å
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Refine LS restraints |
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Xplor file |
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