7AOB | pdb_00007aob

Crystal structure of Thermaerobacter marianensis malate dehydrogenase

PDB DOI: https://doi.org/10.2210/pdb7AOB/pdb

Classification: OXIDOREDUCTASE
Organism(s): Thermaerobacter marianensis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2020-10-14 Released: 2020-10-28
Deposition Author(s): Bertrand, Q., Lasalle, L., Girard, E., Madern, D.
Funding Organization(s): Agence Nationale de la Recherche (ANR)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.12 Å
R-Value Free:
0.205 (Depositor), 0.210 (DCC)
R-Value Work:
0.162 (Depositor), 0.173 (DCC)
R-Value Observed:
0.164 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7AOB

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

Literature

Crystal structure of Thermaerobacter marianensis malate dehydrogenase

Bertrand, Q., Lasalle, L., Girard, E., Madern, D.

To be published.

Macromolecule Content

Total Structure Weight: 134.33 kDa
Atom Count: 10,505
Modeled Residue Count: 1,234
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, C, D	309	Thermaerobacter marianensis	Mutation(s): 0 Gene Names: mdh, Tmar_1268 EC: 1.1.1.37
UniProt
Find proteins for E6SLT2 (Thermaerobacter marianensis (strain ATCC 700841 / DSM 12885 / JCM 10246 / 7p75a)) Explore E6SLT2 Go to UniProtKB: E6SLT2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	E6SLT2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
1PE Query on 1PE Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain O [auth C] MOL2 format, chain O [auth C] mmCIF format, chain O [auth C]	O [auth C]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain O [auth C] Interactions & Density Focus chain O [auth C]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth A] mmCIF format, chain F [auth A] mmCIF format, chain H [auth A]	F [auth A], H [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain H [auth A] Interactions & Density Focus chain F [auth A] Focus chain H [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain M [auth B] SDF format, chain N [auth C] SDF format, chain P [auth D] SDF format, chain Q [auth D] SDF format, chain R [auth D] MOL2 format, chain E [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth C] MOL2 format, chain P [auth D] MOL2 format, chain Q [auth D] MOL2 format, chain R [auth D] mmCIF format, chain E [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain M [auth B] mmCIF format, chain N [auth C] mmCIF format, chain P [auth D] mmCIF format, chain Q [auth D] mmCIF format, chain R [auth D]	E [auth A] I [auth A] J [auth A] K [auth A] M [auth B] E [auth A], I [auth A], J [auth A], K [auth A], M [auth B], N [auth C], P [auth D], Q [auth D], R [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth B] Focus chain N [auth C] Focus chain P [auth D] Focus chain Q [auth D] Focus chain R [auth D] Interactions & Density Focus chain E [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth B] Focus chain N [auth C] Focus chain P [auth D] Focus chain Q [auth D] Focus chain R [auth D]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain L [auth A] MOL2 format, chain L [auth A] mmCIF format, chain L [auth A]	L [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Interactions & Density Focus chain L [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.12 Å
R-Value Free: 0.205 (Depositor), 0.210 (DCC)
R-Value Work: 0.162 (Depositor), 0.173 (DCC)
R-Value Observed: 0.164 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.91	α = 90
b = 150.48	β = 90
c = 153.97	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHASER	phasing
PDB_EXTRACT	data extraction
XDS	data reduction
XSCALE	data scaling

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2020-10-28

Deposition Author(s):

Funding Organization	Location	Grant Number
Agence Nationale de la Recherche (ANR)	France	--

Revision History (Full details and data files)

Version 1.0: 2020-10-28
Type: Initial release
Version 1.1: 2024-01-31
Changes: Data collection, Database references, 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.