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Yorodumi- PDB-7v0d: Crystal structure of halogenase CtcP from Kitasatospora aureofaciens -
+Open data
-Basic information
Entry | Database: PDB / ID: 7v0d | ||||||
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Title | Crystal structure of halogenase CtcP from Kitasatospora aureofaciens | ||||||
Components | Tetracycline 7-halogenase | ||||||
Keywords | OXIDOREDUCTASE / Chlortetracycline / Biosynthesis / Chlorinase / FAD Binding / ANTIBIOTIC | ||||||
Function / homology | tetracycline 7-halogenase / FAD-binding domain / FAD binding domain / antibiotic biosynthetic process / FAD binding / FAD/NAD(P)-binding domain superfamily / oxidoreductase activity / DI(HYDROXYETHYL)ETHER / Tetracycline 7-halogenase Function and homology information | ||||||
Biological species | Kitasatospora aureofaciens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Hou, C. / Tsodikov, O.V. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: Crystal structures and complex formation of halogenase CtcP and FAD reductase CtcQ from the chlortetracycline biosynthetic pathway Authors: Hou, C. / Garneau-Tsodikova, S. / Tsodikov, O.V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7v0d.cif.gz | 229.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7v0d.ent.gz | 182.6 KB | Display | PDB format |
PDBx/mmJSON format | 7v0d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v0/7v0d ftp://data.pdbj.org/pub/pdb/validation_reports/v0/7v0d | HTTPS FTP |
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-Related structure data
Related structure data | 7v0bC 8ct0C 6bzqS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 63077.574 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: The N-terminal GPH is a cloning artifact left after N-terminal tag cleavage Source: (gene. exp.) Kitasatospora aureofaciens (bacteria) / Gene: ctcP, cts4, B6264_18525, HS99_0013305 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1E7MYN1, tetracycline 7-halogenase |
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-Non-polymers , 7 types, 340 molecules
#2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-1PE / | #4: Chemical | ChemComp-CL / | #5: Chemical | #6: Chemical | ChemComp-SO4 / #7: Chemical | ChemComp-EPE / | #8: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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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: 3.7 Å3/Da / Density % sol: 66.76 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 1.6M ammonium sulfate, Hepes pH 7.0, 2% PEG 400 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 16, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. obs: 58486 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 8.6 % / CC1/2: 0.989 / Rmerge(I) obs: 0.147 / Net I/σ(I): 13 |
Reflection shell | Resolution: 2.6→2.64 Å / Num. unique obs: 2868 / CC1/2: 0.895 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6BZQ Resolution: 2.6→35 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.929 / SU B: 9.029 / SU ML: 0.182 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.332 / ESU R Free: 0.233 / 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: 133.14 Å2 / Biso mean: 42.454 Å2 / Biso min: 11.1 Å2
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Refinement step | Cycle: final / Resolution: 2.6→35 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.667 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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