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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.236 (Depositor), 0.246 (DCC)
R-Value Work:
0.178 (Depositor), 0.191 (DCC)
R-Value Observed:
0.181 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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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

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

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	E4QP00
Sequence Annotations 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 [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.236 (Depositor), 0.246 (DCC)
R-Value Work: 0.178 (Depositor), 0.191 (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

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Entry History

Deposition Data

Released Date: 2015-03-18

Deposition Author(s):

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.