+Open data
-Basic information
Entry | Database: PDB / ID: 6g71 | ||||||
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Title | Structure of CYP1232A24 from Arthrobacter sp. | ||||||
Components | Cytochrome P450 | ||||||
Keywords | OXIDOREDUCTASE / P450 / heme / demethylase | ||||||
Function / homology | Function and homology information salicylate 1-monooxygenase / salicylate 1-monooxygenase activity / iron ion binding / heme binding Similarity search - Function | ||||||
Biological species | Arthrobacter (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Dubiel, P. / Sharma, M. / Klenk, J. / Hauer, B. / Grogan, G. | ||||||
Citation | Journal: J.Biochem. / Year: 2019 Title: Identification and characterization of cytochrome P450 1232A24 and 1232F1 from Arthrobacter sp. and their role in the metabolic pathway of papaverine. Authors: Klenk, J.M. / Fischer, M.P. / Dubiel, P. / Sharma, M. / Rowlinson, B. / Grogan, G. / Hauer, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6g71.cif.gz | 97.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6g71.ent.gz | 71.3 KB | Display | PDB format |
PDBx/mmJSON format | 6g71.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g7/6g71 ftp://data.pdbj.org/pub/pdb/validation_reports/g7/6g71 | HTTPS FTP |
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-Related structure data
Related structure data | 2vz7S 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
#1: Protein | Mass: 44916.750 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arthrobacter (bacteria) / Plasmid: pET-YSBLIC-3C / Production host: Escherichia coli (E. coli) References: UniProt: A0A4V8GZW5*PLUS, salicylate 1-monooxygenase | ||
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#2: Chemical | ChemComp-PP9 / | ||
#3: Chemical | ChemComp-FE / | ||
#4: Chemical | #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: 2.35 Å3/Da / Density % sol: 47.6 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M Bis-tris pH 6.5; 20% PEG 5000 MME |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 9, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91587 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→52.92 Å / Num. obs: 44239 / % possible obs: 97.6 % / Redundancy: 4.1 % / Biso Wilson estimate: 18 Å2 / CC1/2: 0.94 / Rmerge(I) obs: 0.19 / Rpim(I) all: 0.16 / Net I/σ(I): 4.5 |
Reflection shell | Resolution: 1.7→1.74 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 3185 / CC1/2: 0.55 / Rpim(I) all: 0.61 / % possible all: 95.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2VZ7 Resolution: 1.7→50.42 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.943 / SU B: 3.592 / SU ML: 0.108 / Cross valid method: THROUGHOUT / ESU R: 0.112 / ESU R Free: 0.112 / 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: 25.716 Å2
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Refinement step | Cycle: 1 / Resolution: 1.7→50.42 Å
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Refine LS restraints |
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