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Yorodumi- PDB-6nbl: Cytochrome P450cam-putidaredoxin complex bound to camphor and cyanide -
+Open data
-Basic information
Entry | Database: PDB / ID: 6nbl | ||||||
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Title | Cytochrome P450cam-putidaredoxin complex bound to camphor and cyanide | ||||||
Components |
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Keywords | OXIDOREDUCTASE / ELECTRON TRANSPORT | ||||||
Function / homology | Function and homology information P450-containing electron transport chain / camphor 5-monooxygenase / camphor 5-monooxygenase activity / (+)-camphor catabolic process / cholest-4-en-3-one 26-monooxygenase activity / steroid hydroxylase activity / cholesterol catabolic process / 2 iron, 2 sulfur cluster binding / iron ion binding / heme binding ...P450-containing electron transport chain / camphor 5-monooxygenase / camphor 5-monooxygenase activity / (+)-camphor catabolic process / cholest-4-en-3-one 26-monooxygenase activity / steroid hydroxylase activity / cholesterol catabolic process / 2 iron, 2 sulfur cluster binding / iron ion binding / heme binding / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Pseudomonas putida (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | ||||||
Authors | Follmer, A.H. / Tripathi, S.M. / Poulos, T.L. | ||||||
Funding support | United States, 1items
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Citation | Journal: J. Am. Chem. Soc. / Year: 2019 Title: Ligand and Redox Partner Binding Generates a New Conformational State in Cytochrome P450cam (CYP101A1). Authors: Follmer, A.H. / Tripathi, S. / Poulos, T.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6nbl.cif.gz | 226.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6nbl.ent.gz | 179.5 KB | Display | PDB format |
PDBx/mmJSON format | 6nbl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nb/6nbl ftp://data.pdbj.org/pub/pdb/validation_reports/nb/6nbl | HTTPS FTP |
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-Related structure data
Related structure data | 4jwsS 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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2 |
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Unit cell |
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-Components
-Protein , 2 types, 4 molecules ABCD
#1: Protein | Mass: 46597.715 Da / Num. of mol.: 2 / Mutation: C334A, K344C, C59S, C86S, C137S, C268S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: camC, cyp101 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P00183, camphor 5-monooxygenase #2: Protein | Mass: 12229.779 Da / Num. of mol.: 2 / Mutation: D19C, C74S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: camB / Production host: Escherichia coli (E. coli) / References: UniProt: P00259 |
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-Non-polymers , 7 types, 407 molecules
#3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | #7: Chemical | #8: Chemical | #9: 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: 2.3 Å3/Da / Density % sol: 46.46 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 0.2 M calcium acetate hydrate, 14-22% PEG3350, pH 7.4, 50 mM KCN |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 28, 2013 |
Radiation | Monochromator: Si(111) Side scattering bent cube-root I-beam single crystal Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→40.603 Å / Num. obs: 54970 / % possible obs: 96.26 % / Redundancy: 2 % / Biso Wilson estimate: 31.8668364658 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.04968 / Rpim(I) all: 0.04968 / Rsym value: 0.07026 / Net I/σ(I): 10.42 |
Reflection shell | Resolution: 2.15→2.227 Å / Redundancy: 2 % / Rmerge(I) obs: 0.3476 / Mean I/σ(I) obs: 2.46 / Num. unique obs: 5453 / CC1/2: 0.632 / Rpim(I) all: 0.3476 / Rrim(I) all: 0.4916 / % possible all: 96.33 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4JWS Resolution: 2.15→40.603 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.23
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.15→40.603 Å
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Refine LS restraints |
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LS refinement shell |
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