[English] 日本語
Yorodumi- PDB-4udq: Crystal structure of 5-hydroxymethylfurfural oxidase (HMFO) in th... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4udq | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of 5-hydroxymethylfurfural oxidase (HMFO) in the reduced 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 / OTHER / Resolution: 1.6 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4udq.cif.gz | 223.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4udq.ent.gz | 179 KB | Display | PDB format |
PDBx/mmJSON format | 4udq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ud/4udq ftp://data.pdbj.org/pub/pdb/validation_reports/ud/4udq | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
| ||||||||
Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.992, -0.1131, 0.05635), 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 (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: E4QP00 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.96 Å3/Da / Density % sol: 37 % / Description: NONE |
---|---|
Crystal grow | Details: 22% W/V PEG3350, 200 MM MAGNESIUM FORMATE |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 19, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→22 Å / Num. obs: 114344 / % possible obs: 99.2 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 4.8 |
Reflection shell | Resolution: 1.6→1.63 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 1.2 / % possible all: 98.3 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: OTHER Starting model: NONE Resolution: 1.6→72.47 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.939 / SU B: 2.721 / SU ML: 0.089 / Cross valid method: THROUGHOUT / ESU R: 0.095 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.537 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→72.47 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|