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Yorodumi- PDB-2wdw: The Native Crystal Structure of the Primary Hexose Oxidase (Dbv29... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2wdw | ||||||
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Title | The Native Crystal Structure of the Primary Hexose Oxidase (Dbv29) in Antibiotic A40926 Biosynthesis | ||||||
Components | PUTATIVE HEXOSE OXIDASE | ||||||
Keywords | OXIDOREDUCTASE / FAD / FLAVOPROTEIN / HEXOSE OXIDASE | ||||||
Function / homology | Function and homology information acyltransferase activity / glycosyltransferase activity / FAD binding / monooxygenase activity Similarity search - Function | ||||||
Biological species | NONOMURAEA SP. ATCC 39727 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.21 Å | ||||||
Authors | Liu, Y.-C. / Li, Y.-S. / Lyu, S.-Y. / Chen, Y.-H. / Chan, H.-C. / Huang, C.-J. / Huang, Y.-T. / Chen, G.-H. / Chou, C.-C. / Tsai, M.-D. / Li, T.-L. | ||||||
Citation | Journal: Nat.Chem.Biol. / Year: 2011 Title: Interception of Teicoplanin Oxidation Intermediates Yields New Antimicrobial Scaffolds Authors: Liu, Y.-C. / Li, Y.-S. / Lyu, S.-Y. / Hsu, L.-J. / Chen, Y.-H. / Huang, Y.-T. / Chan, H.-C. / Huang, C.-J. / Chen, G.-H. / Chou, C.-C. / Tsai, M.-D. / Li, T.-L. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2wdw.cif.gz | 197.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wdw.ent.gz | 157 KB | Display | PDB format |
PDBx/mmJSON format | 2wdw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wd/2wdw ftp://data.pdbj.org/pub/pdb/validation_reports/wd/2wdw | HTTPS FTP |
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-Related structure data
Related structure data | 5awvC 2ipiS 2wdx 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: 57059.012 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) NONOMURAEA SP. ATCC 39727 (bacteria) / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K-12 / References: UniProt: Q7WZ62, alcohol oxidase #2: Chemical | #3: 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: 2.08 Å3/Da / Density % sol: 40.81 % / Description: NONE |
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Crystal grow | pH: 6.5 Details: PROTEIN WAS CRYSTALLIZED FROM 30% PEG 550 MME, 0.05M CALCIUM CHLORIDE, 0.1M BIS TRIS, PH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.9731 |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 25, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9731 Å / Relative weight: 1 |
Reflection | Resolution: 3.21→30 Å / Num. obs: 17824 / % possible obs: 95.7 % / Observed criterion σ(I): 2 / Redundancy: 9.7 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 24.8 |
Reflection shell | Resolution: 3.21→3.32 Å / Redundancy: 9.8 % / Rmerge(I) obs: 0.16 / Mean I/σ(I) obs: 17 / % possible all: 92 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2IPI Resolution: 3.21→29.54 Å / Cor.coef. Fo:Fc: 0.882 / Cor.coef. Fo:Fc free: 0.83 / SU B: 27.218 / SU ML: 0.458 / Cross valid method: THROUGHOUT / ESU R Free: 0.658 / 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: 28.94 Å2
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Refinement step | Cycle: LAST / Resolution: 3.21→29.54 Å
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Refine LS restraints |
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