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Yorodumi- PDB-6kzt: Crystal structure of cytochrome P450mel 107F1 with biaryl couplin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6kzt | ||||||||||||
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Title | Crystal structure of cytochrome P450mel 107F1 with biaryl coupling reactivity | ||||||||||||
Components | Cytochrome P-450 | ||||||||||||
Keywords | OXIDOREDUCTASE / biaryl coupling / Heme / P450 | ||||||||||||
Function / homology | Function and homology information Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen / 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 | Streptomyces griseus (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å | ||||||||||||
Authors | Hou, X.D. / Rao, Y.J. / Icyishaka, P. / Li, C.X. / Lou, J.L. | ||||||||||||
Funding support | China, 3items
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Citation | Journal: To Be Published Title: Crystallization and X-ray analysis of cytochrome P450mel 107F1 with biaryl coupling reactivity Authors: Hou, X.D. / Rao, Y.J. / Icyishaka, P. / Li, C.X. / Lou, J.L. / Liu, C.M. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6kzt.cif.gz | 94.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6kzt.ent.gz | 69.6 KB | Display | PDB format |
PDBx/mmJSON format | 6kzt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6kzt_validation.pdf.gz | 759.2 KB | Display | wwPDB validaton report |
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Full document | 6kzt_full_validation.pdf.gz | 766.7 KB | Display | |
Data in XML | 6kzt_validation.xml.gz | 16.7 KB | Display | |
Data in CIF | 6kzt_validation.cif.gz | 21.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kz/6kzt ftp://data.pdbj.org/pub/pdb/validation_reports/kz/6kzt | HTTPS FTP |
-Related structure data
Related structure data | 6kzsC 2d09S 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: 46636.938 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces griseus (bacteria) / Gene: P-450mel, p450-mel, NCTC13033_01802 / Production host: Escherichia coli (E. coli) References: UniProt: Q4H2B8, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen |
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#2: Chemical | ChemComp-HEM / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.36 Å3/Da / Density % sol: 63.34 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 18% v/v 2-Propanol, 0.1 M Sodium citrate tribasic dihydrate pH 5.5, 20% w/v Polyethylene glycol 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.979 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 20, 2018 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.5→50 Å / Num. obs: 7557 / % possible obs: 100 % / Redundancy: 20 % / Rmerge(I) obs: 0.236 / Rpim(I) all: 0.054 / Rrim(I) all: 0.242 / Χ2: 0.986 / Net I/σ(I): 3.5 / Num. measured all: 151136 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2d09 Resolution: 3.5→42.17 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.85 / SU B: 31.062 / SU ML: 0.464 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.699 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 114.23 Å2 / Biso mean: 49.89 Å2 / Biso min: 27.77 Å2
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Refinement step | Cycle: final / Resolution: 3.5→42.17 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.505→3.596 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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