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Yorodumi- PDB-4udp: Crystal structure of 5-hydroxymethylfurfural oxidase (HMFO) in th... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4udp | ||||||
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Title | Crystal structure of 5-hydroxymethylfurfural oxidase (HMFO) in the oxidized state | ||||||
Components | GLUCOSE-METHANOL-CHOLINE OXIDOREDUCTASE | ||||||
Keywords | OXIDOREDUCTASE / ENZYME / OXIDASE / BIOCATALYSIS / PROTEIN ENGINEERING | ||||||
Function / homology | Function and homology information 5-(hydroxymethyl)furfural oxidase / Oxidoreductases; Acting on a sulfur group of donors; With oxygen as acceptor / oxidoreductase activity, acting on a sulfur group of donors, oxygen as acceptor / oxidoreductase activity, acting on the CH-OH group of donors, oxygen as acceptor / FAD binding Similarity search - Function | ||||||
Biological species | Methylovorus sp. MP688 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Dijkman, W. / Binda, C. / Fraaije, M. / Mattevi, A. | ||||||
Citation | Journal: Acs Catalysis / Year: 2015 Title: Structure-Based Enzyme Tailoring of 5-Hydroxymethylfurfural Oxidase Authors: Dijkman, W.P. / Binda, C. / Fraaije, M.W. / Mattevi, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4udp.cif.gz | 212.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4udp.ent.gz | 169 KB | Display | PDB format |
PDBx/mmJSON format | 4udp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ud/4udp ftp://data.pdbj.org/pub/pdb/validation_reports/ud/4udp | HTTPS FTP |
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-Related structure data
Related structure data | 4udqC 4udrC 2jbvS 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.9937, -0.09548, 0.05934), Vector: |
-Components
#1: Protein | Mass: 57076.109 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methylovorus sp. MP688 (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: E4QP00 #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: 1.92 Å3/Da / Density % sol: 36 % / Description: NONE |
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Crystal grow | Details: 16-22% W/V PEG3350, 200 MM MAGNESIUM FORMATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.976 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 15, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 67679 / % possible obs: 99.9 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 9 |
Reflection shell | Resolution: 1.9→1.94 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.97 / Mean I/σ(I) obs: 0.85 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2JBV Resolution: 1.9→72.3 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.926 / SU B: 4.939 / SU ML: 0.14 / Cross valid method: THROUGHOUT / ESU R: 0.179 / ESU R Free: 0.164 / 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: 24.92 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→72.3 Å
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Refine LS restraints |
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