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- PDB-4udp: Crystal structure of 5-hydroxymethylfurfural oxidase (HMFO) in th... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4udp | ||||||
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Title | Crystal structure of 5-hydroxymethylfurfural oxidase (HMFO) in the oxidized state | ||||||
![]() | GLUCOSE-METHANOL-CHOLINE OXIDOREDUCTASE | ||||||
![]() | OXIDOREDUCTASE / ENZYME / OXIDASE / BIOCATALYSIS / PROTEIN ENGINEERING | ||||||
Function / homology | ![]() 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 / choline dehydrogenase activity / oxidoreductase activity, acting on the CH-OH group of donors, oxygen as acceptor / glycine betaine biosynthetic process from choline / FAD binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Dijkman, W. / Binda, C. / Fraaije, M. / Mattevi, A. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 212.3 KB | Display | ![]() |
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PDB format | ![]() | 169 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 934 KB | Display | ![]() |
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Full document | ![]() | 947.6 KB | Display | |
Data in XML | ![]() | 41 KB | Display | |
Data in CIF | ![]() | 57.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4udqC ![]() 4udrC ![]() 2jbvS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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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: |
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Components
#1: Protein | Mass: 57076.109 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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