30IZ | pdb_000030iz

Ignicoccus islandicus malate dehydrogenase V27A mutant

PDB DOI: https://doi.org/10.2210/pdb30IZ/pdb

Classification: OXIDOREDUCTASE
Organism(s): Ignicoccus islandicus
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2026-04-29 Released: 2026-07-22
Deposition Author(s): Engilberge, S., Coquille, S., Madern, D.
Funding Organization(s): Agence Nationale de la Recherche (ANR)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.02 Å
R-Value Free:
0.242 (Depositor), 0.238 (DCC)
R-Value Work:
0.189 (Depositor), 0.190 (DCC)
R-Value Observed:
0.192 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.0 of the entry. See complete history.

Literature

Ignicoccus islandicus malate dehydrogenase V27A mutant

Coquille, S., Engilberge, S., Madern, D.

To be published.

Macromolecule Content

Total Structure Weight: 133.94 kDa
Atom Count: 9,935
Modeled Residue Count: 1,228
Deposited Residue Count: 1,236
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Malate dehydrogenase	A, B [auth D], C [auth B], D [auth C]	309	Ignicoccus islandicus	Mutation(s): 1 Gene Names: EYM_03995
UniProt
Find proteins for A0A0U3FQH7 (Ignicoccus islandicus DSM 13165) Explore A0A0U3FQH7 Go to UniProtKB: A0A0U3FQH7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0U3FQH7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MLI Query on MLI Download:Ideal Coordinates CCD File SDF format, chain F [auth D] SDF format, chain E [auth A] MOL2 format, chain F [auth D] MOL2 format, chain E [auth A] mmCIF format, chain F [auth D] mmCIF format, chain E [auth A]	E [auth A], F [auth D]	MALONATE ION C₃ H₂ O₄ OFOBLEOULBTSOW-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain F [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.02 Å
R-Value Free: 0.242 (Depositor), 0.238 (DCC)
R-Value Work: 0.189 (Depositor), 0.190 (DCC)
R-Value Observed: 0.192 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.865	α = 90
b = 107.944	β = 90
c = 143.096	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-07-22

Deposition Author(s):

Funding Organization	Location	Grant Number
Agence Nationale de la Recherche (ANR)	France	ANR-21-CE44-0034-01

Revision History (Full details and data files)

Version 1.0: 2026-07-22
Type: Initial release

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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.