6H9S | pdb_00006h9s

Crystal dimeric structure of Petrotoga mobilis lactate dehydrogenase with NADH

PDB DOI: https://doi.org/10.2210/pdb6H9S/pdb

Classification: OXIDOREDUCTASE
Organism(s): Petrotoga mobilis SJ95
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2018-08-06 Released: 2018-08-22
Deposition Author(s): Roche, J., Engilberge, S., Girard, E., Madern, D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.197 (Depositor), 0.197 (DCC)
R-Value Work:
0.169 (Depositor), 0.172 (DCC)
R-Value Observed:
0.171 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Structure of Petrotoga mobilis lactate dehydrogenase at 1.9 Angstrom resolution

Roche, J., Engilberge, S., Girard, E., Madern, D.

To be published.

Macromolecule Content

Total Structure Weight: 68.1 kDa
Atom Count: 4,767
Modeled Residue Count: 581
Deposited Residue Count: 614
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-lactate dehydrogenase	A, B	307	Petrotoga mobilis SJ95	Mutation(s): 0 Gene Names: ldh, Pmob_1893 EC: 1.1.1.27
UniProt
Find proteins for A9BGZ9 (Petrotoga mobilis (strain DSM 10674 / SJ95)) Explore A9BGZ9 Go to UniProtKB: A9BGZ9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A9BGZ9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD Query on NAD Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-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: 0.197 (Depositor), 0.197 (DCC)
R-Value Work: 0.169 (Depositor), 0.172 (DCC)
R-Value Observed: 0.171 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.268	α = 90
b = 103.739	β = 107.25
c = 90.7	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2018-08-22

Deposition Author(s):

Funding Organization	Location	Grant Number
	France	--

Revision History (Full details and data files)

Version 1.0: 2018-08-22
Type: Initial release
Version 1.1: 2024-01-17
Changes: Data collection, Database references, Refinement description
Version 1.2: 2024-10-23
Changes: Structure summary

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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.