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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.197 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.169 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.171 (Depositor) 

Starting Model: experimental

Literature

Structure of Petrotoga mobilis lactate dehydrogenase at 1.9 Angstrom resolution

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

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 generated by PISA (software)

Biological Assembly Evidence: gel filtration

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

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	C [auth A], D [auth B]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.197 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.169 (Depositor), 0.170 (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

Entry History & Funding Information

Deposition Data

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

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Funding Organization	Location	Grant Number
	France	--

Revision History  

• 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