4UDP | pdb_00004udp

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

• PDB DOI: https://doi.org/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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.236 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.178 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Starting Model: experimental

Literature

Structure-Based Enzyme Tailoring of 5-Hydroxymethylfurfural Oxidase

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

(2015) ACS Catal 5: 1833

• DOI: https://doi.org/10.1021/ACSCATAL.5B00031

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 115.72 kDa 
• Atom Count: 8,311 
• Modeled Residue Count: 1,032 
• Deposited Residue Count: 1,062 
• Unique protein chains: 1

Macromolecules

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	C [auth A], D [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.236 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.178 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

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

Entry History 

Deposition Data

• Released Date: 2015-03-18 
Deposition Author(s): Dijkman, W., Binda, C., Fraaije, M., Mattevi, A.

Revision History  

• Version 1.0: 2015-03-18
  Type: Initial release
  
• Version 1.1: 2018-03-07
  Changes: Data collection, Source and taxonomy
• Version 1.2: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description