4UDQ | pdb_00004udq

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

PDB DOI: https://doi.org/10.2210/pdb4UDQ/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: 1.60 Å
R-Value Free:
0.216 (Depositor), 0.226 (DCC)
R-Value Work:
0.168 (Depositor), 0.180 (DCC)
R-Value Observed:
0.171 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

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

Macromolecule Content

Total Structure Weight: 115.82 kDa
Atom Count: 8,832
Modeled Residue Count: 1,050
Deposited Residue Count: 1,062
Unique protein chains: 1

Macromolecules

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| 3D Structure

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 2 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 E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth B] mmCIF format, chain C [auth A] mmCIF format, chain E [auth B]	C [auth A], E [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]
FMT Query on FMT Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth B] MOL2 format, chain D [auth A] MOL2 format, chain F [auth B] mmCIF format, chain D [auth A] mmCIF format, chain F [auth B]	D [auth A], F [auth B]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.216 (Depositor), 0.226 (DCC)
R-Value Work: 0.168 (Depositor), 0.180 (DCC)
R-Value Observed: 0.171 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.55	α = 90
b = 121.83	β = 91.4
c = 72.49	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
Aimless	data scaling
REFMAC	phasing

Structure Validation

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Ligand Structure Quality Assessment

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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: 2024-05-08
Changes: Data collection, Database references, Derived calculations, Other

4UDQ | pdb_00004udq

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

Literature

Structure-Based Enzyme Tailoring of 5-Hydroxymethylfurfural Oxidase

Biological Assembly 1

Biological Assembly 2

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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