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Yorodumi- PDB-4yzr: Bacillus subtilis 168 Bacillaene Polyketide Synthase (PKS) Cytoch... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4yzr | ||||||
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Title | Bacillus subtilis 168 Bacillaene Polyketide Synthase (PKS) Cytochrome P450 PksS | ||||||
Components | Polyketide biosynthesis cytochrome P450 PksS | ||||||
Keywords | OXIDOREDUCTASE / cytochrome P450 / Bacillaene biosynthesis / Polyketide Synthase | ||||||
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 / antibiotic biosynthetic process / monooxygenase activity / membrane => GO:0016020 / iron ion binding / heme binding / plasma membrane Similarity search - Function | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å | ||||||
Authors | Race, P.R. / Zulkepli, A.Z. / Anderson, R.J.L. | ||||||
Citation | Journal: To Be Published Title: Bacillus subtilis 168 Bacillaene Polyketide Synthase (PKS) Cytochrome P450 PksS Authors: Race, P.R. / Zulkepli, A.Z. / Anderson, R.J.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4yzr.cif.gz | 102.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4yzr.ent.gz | 76.3 KB | Display | PDB format |
PDBx/mmJSON format | 4yzr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4yzr_validation.pdf.gz | 825.6 KB | Display | wwPDB validaton report |
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Full document | 4yzr_full_validation.pdf.gz | 836.9 KB | Display | |
Data in XML | 4yzr_validation.xml.gz | 20.8 KB | Display | |
Data in CIF | 4yzr_validation.cif.gz | 30.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yz/4yzr ftp://data.pdbj.org/pub/pdb/validation_reports/yz/4yzr | HTTPS FTP |
-Related structure data
Related structure data | 3a50S 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: 46797.867 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: pksS, BSU17230 / Plasmid: pET151/D-TOPO / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: O31785, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen |
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#2: Chemical | ChemComp-HIS / |
#3: Chemical | ChemComp-HEM / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.69 Å3/Da / Density % sol: 54.14 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: Morpheus TM screen Condition B1: 0.09 M Halogen, 0.1 M Imidazole, MES pH 6.5, 30% P550MME-P20K PH range: 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 17, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→46.65 Å / Num. obs: 98866 / % possible obs: 99.9 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 10.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3A50 Resolution: 1.35→46.5 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.949 / SU B: 0.937 / SU ML: 0.038 / Cross valid method: THROUGHOUT / ESU R: 0.053 / ESU R Free: 0.056 / 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: 19.476 Å2
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Refinement step | Cycle: 1 / Resolution: 1.35→46.5 Å
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Refine LS restraints |
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