+Open data
-Basic information
Entry | Database: PDB / ID: 6j39 | ||||||
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Title | Crystal structure of CmiS2 with inhibitor | ||||||
Components | FAD-dependent glycine oxydase | ||||||
Keywords | OXIDOREDUCTASE/INHIBITOR / Flavoenzyme / Polyketide biosynthesis / OXIDOREDUCTASE / OXIDOREDUCTASE-INHIBITOR complex | ||||||
Function / homology | Function and homology information thiamine diphosphate biosynthetic process / flavin adenine dinucleotide binding / oxidoreductase activity Similarity search - Function | ||||||
Biological species | Streptomyces sp. MJ635-86F5 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å | ||||||
Authors | Kawasaki, D. / Chisuga, T. / Miyanaga, A. / Kudo, F. / Eguchi, T. | ||||||
Citation | Journal: Biochemistry / Year: 2019 Title: Structural Analysis of the Glycine Oxidase Homologue CmiS2 Reveals a Unique Substrate Recognition Mechanism for Formation of a beta-Amino Acid Starter Unit in Cremimycin Biosynthesis. Authors: Kawasaki, D. / Chisuga, T. / Miyanaga, A. / Kudo, F. / Eguchi, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6j39.cif.gz | 153.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6j39.ent.gz | 117.4 KB | Display | PDB format |
PDBx/mmJSON format | 6j39.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j3/6j39 ftp://data.pdbj.org/pub/pdb/validation_reports/j3/6j39 | HTTPS FTP |
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-Related structure data
Related structure data | 6j38C 1ryiS 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: HIS / Beg label comp-ID: HIS / End auth comp-ID: PHE / End label comp-ID: PHE / Refine code: 0 / Auth seq-ID: 2 - 368 / Label seq-ID: 22 - 388
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-Components
#1: Protein | Mass: 41262.020 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces sp. MJ635-86F5 (bacteria) / Gene: cmiS2 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: X5IYZ1 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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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: 2.69 Å3/Da / Density % sol: 54.24 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: MES-Na, PEG3350, hexaamminecobalt(III) chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 21, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→50 Å / Num. obs: 32256 / % possible obs: 99.9 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 13.8 |
Reflection shell | Resolution: 2.45→2.55 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.416 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 3633 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1RYI Resolution: 2.45→44.36 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.911 / SU B: 13.418 / SU ML: 0.274 / Cross valid method: THROUGHOUT / ESU R: 0.434 / ESU R Free: 0.287 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 53.557 Å2
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Refinement step | Cycle: 1 / Resolution: 2.45→44.36 Å
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Refine LS restraints |
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