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Yorodumi- PDB-5hyg: CmlI (peroxo bound state), arylamine oxygenase of chloramphenicol... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5hyg | |||||||||
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Title | CmlI (peroxo bound state), arylamine oxygenase of chloramphenicol biosynthetic pathway | |||||||||
Components | Uncharacterized protein | |||||||||
Keywords | METAL BINDING PROTEIN / Oxygen activation / Non-heme iron / Diiron cluster / Antibiotic biosynthesis | |||||||||
Function / homology | Function and homology information alpha-N-dichloroacetyl-p-aminophenylserinol N-oxygenase / antibiotic biosynthetic process / oxidoreductase activity / metal ion binding Similarity search - Function | |||||||||
Biological species | Streptomyces venezuelae (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 Å | |||||||||
Authors | Knoot, C.J. / Lipscomb, J.D. | |||||||||
Funding support | United States, 2items
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Citation | Journal: J.Biol.Inorg.Chem. / Year: 2016 Title: Crystal structure of CmlI, the arylamine oxygenase from the chloramphenicol biosynthetic pathway. Authors: Knoot, C.J. / Kovaleva, E.G. / Lipscomb, J.D. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5hyg.cif.gz | 73.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5hyg.ent.gz | 53.4 KB | Display | PDB format |
PDBx/mmJSON format | 5hyg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hy/5hyg ftp://data.pdbj.org/pub/pdb/validation_reports/hy/5hyg | HTTPS FTP |
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-Related structure data
Related structure data | 5hyhC 3chhS C: citing same article (ref.) 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 36162.516 Da / Num. of mol.: 1 / Fragment: residues 33-339 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces venezuelae (strain ATCC 10712 / CBS 650.69 / DSM 40230 / JCM 4526 / NBRC 13096 / PD 04745) (bacteria) Strain: ATCC 10712 / CBS 650.69 / DSM 40230 / JCM 4526 / NBRC 13096 / PD 04745 Gene: SVEN_0924 / Plasmid: pVP91A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: F2RB83 | ||||||
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#2: Chemical | #3: Chemical | ChemComp-TLA / | #4: Chemical | ChemComp-PEO / | #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: 1.9 Å3/Da / Density % sol: 35 % / Description: Triangular |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 1500, L-(+)-ammonium tartrate / PH range: 6.5-6.8 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97926 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 27, 2015 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97926 Å / Relative weight: 1 |
Reflection | Resolution: 2.03→50 Å / Num. obs: 15532 / % possible obs: 88.4 % / Redundancy: 5.5 % / Biso Wilson estimate: 29.3 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 29 |
Reflection shell | Resolution: 2.03→2.07 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.408 / Mean I/σ(I) obs: 6.9 / % possible all: 82.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3CHH Resolution: 2.03→22 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.917 / SU B: 4.657 / SU ML: 0.129 / Cross valid method: THROUGHOUT / ESU R: 0.287 / ESU R Free: 0.227 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.529 Å2
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Refinement step | Cycle: LAST / Resolution: 2.03→22 Å
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