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Yorodumi- PDB-4xac: Crystal Structure of EvdO2 from Micromonospora carbonacea var. au... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4xac | ||||||
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Title | Crystal Structure of EvdO2 from Micromonospora carbonacea var. aurantiaca complexed with 2-oxoglutarate | ||||||
Components | EvdO2 | ||||||
Keywords | OXIDOREDUCTASE / double stranded beta helix | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Micromonospora carbonacea (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å | ||||||
Authors | McCulloch, K.M. / McCranie, E.K. / Sarwar, M. / Mathieu, J.L. / Gitschlag, B.L. / Du, Y. / Bachmann, B.O. / Iverson, T.M. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2015 Title: Oxidative cyclizations in orthosomycin biosynthesis expand the known chemistry of an oxygenase superfamily. Authors: McCulloch, K.M. / McCranie, E.K. / Smith, J.A. / Sarwar, M. / Mathieu, J.L. / Gitschlag, B.L. / Du, Y. / Bachmann, B.O. / Iverson, T.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4xac.cif.gz | 115.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4xac.ent.gz | 89.2 KB | Display | PDB format |
PDBx/mmJSON format | 4xac.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4xac_validation.pdf.gz | 447.2 KB | Display | wwPDB validaton report |
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Full document | 4xac_full_validation.pdf.gz | 447.3 KB | Display | |
Data in XML | 4xac_validation.xml.gz | 12.2 KB | Display | |
Data in CIF | 4xac_validation.cif.gz | 16.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xa/4xac ftp://data.pdbj.org/pub/pdb/validation_reports/xa/4xac | HTTPS FTP |
-Related structure data
Related structure data | 4xaaC 4xabSC 4xbzC 4xc9C 4xcaC 4xcbC 4zpiC 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: 28611.170 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Micromonospora carbonacea (bacteria) / Variant: var. aurantiaca / Plasmid: pET28a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A0M3KL01*PLUS |
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#2: Chemical | ChemComp-NI / |
#3: Chemical | ChemComp-IMD / |
#4: Chemical | ChemComp-AKG / |
#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: 2.05 Å3/Da / Density % sol: 40.12 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 38% PEG 8000, 100 mM imidazole, 250 mM NaCl. Crystals soaked 30 min in 20 mM 2-oxoglutarate solution |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.127 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 7, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.127 Å / Relative weight: 1 |
Reflection | Resolution: 1.87→50 Å / Num. obs: 19714 / % possible obs: 97.2 % / Redundancy: 5.7 % / Biso Wilson estimate: 25.9 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 14 |
Reflection shell | Resolution: 1.87→1.94 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.324 / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4XAB Resolution: 1.87→37.99 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 20 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.18 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.87→37.99 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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