Macromolecule Content

Total Structure Weight: 115.72 kDa
Atom Count: 8311
Residue Count: 1032
Unique protein chains: 1

4UDP

Crystal structure of 5-hydroxymethylfurfural oxidase (HMFO) in the oxidized state

DOI: 10.2210/pdb4UDP/pdb

Classification: OXIDOREDUCTASE
Organism(s): Methylovorus sp. MP688
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2014-12-11 Released: 2015-03-18
Deposition Author(s): Dijkman, W., Binda, C., Fraaije, M., Mattevi, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.236
R-Value Work: 0.178
R-Value Observed: 0.181

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Structure-Based Enzyme Tailoring of 5-Hydroxymethylfurfural Oxidase

Dijkman, W.P., Binda, C., Fraaije, M.W., Mattevi, A.

(2015) ACS Catal 5: 1833

Macromolecules

Find similar proteins by:

(by identity cutoff) | Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GLUCOSE-METHANOL-CHOLINE OXIDOREDUCTASE	A, B	531	Methylovorus sp. MP688	Mutation(s): 0 Gene Names: MPQ_0130 EC: 1.1.3.47 (UniProt), 1.8.3 (UniProt)
Find proteins for E4QP00 (Methylovorus sp. (strain MP688)) Explore E4QP00 Go to UniProtKB: E4QP00
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download Ideal Coordinates CCD File SDF format, chain C [A] SDF format, chain D [B] MOL2 format, chain C [A] MOL2 format, chain D [B]	A, B	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Ligand Interaction

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.236
R-Value Work: 0.178
R-Value Observed: 0.181
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.964	α = 90
b = 120.907	β = 91.39
c = 72.322	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
BALBES	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Deposited Date: 2014-12-11
Released Date: 2015-03-18

Deposition Author(s):

Revision History

Version 1.0: 2015-03-18
Type: Initial release
Version 1.1: 2018-03-07
Changes: Data collection, Source and taxonomy

RCSB PDB is funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.