- PDB-4udr: Crystal structure of the H467A mutant of 5-hydroxymethylfurfural ... -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 4udr
Title
Crystal structure of the H467A mutant of 5-hydroxymethylfurfural oxidase (HMFO)
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 / 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
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 1 Å / Relative weight: 1
Reflection
Resolution: 1.6→21 Å / Num. obs: 115432 / % possible obs: 98.2 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 4.8
Reflection shell
Resolution: 1.6→1.63 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 1.5 / % possible all: 95.2
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Processing
Software
Name
Version
Classification
REFMAC
5.8.0073
refinement
MOSFLM
datareduction
Aimless
datascaling
REFMAC
phasing
Refinement
Method to determine structure: OTHER Starting model: NONE Resolution: 1.6→73.26 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.927 / SU B: 2.56 / SU ML: 0.086 / Cross valid method: THROUGHOUT / ESU R: 0.1 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.21753
5538
4.8 %
RANDOM
Rwork
0.17568
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obs
0.17768
109850
97.99 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å