Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 87.27 kDa 
• Atom Count: 6576 
• Modelled Residue Count: 717 
• Deposited Residue Count: 770 
• Unique protein chains: 1

2G8Y

The structure of a putative malate/lactate dehydrogenase from E. coli.

• PDB DOI: 10.2210/pdb2G8Y/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2006-03-03 Released: 2006-04-25 
• Deposition Author(s): Cuff, M.E., Skarina, T., Edwards, A., Savchenko, A., Cymborowski, M., Minor, W., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.186 
• R-Value Work: 0.158 
• R-Value Observed: 0.159 

Literature

The structure of a putative malate/lactate dehydrogenase from E. coli.

Cuff, M.E., Skarina, T., Edwards, A., Savchenko, A., Cymborowski, M., Minor, W., Joachimiak, A.

To be published.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Malate/L-lactate dehydrogenases	A, B	385	Escherichia coli K-12	Mutation(s): 9  Gene Names: ybiC, hcxB, b0801, JW0786 EC: 1.1.1 (UniProt), 1.1.1.237 (UniProt)
UniProt
Find proteins for P30178 (Escherichia coli (strain K12)) Explore P30178  Go to UniProtKB:  P30178

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	F [auth A], R [auth B]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
1PE	L [auth A]	PENTAETHYLENE GLYCOL C10 H22 O6 JLFNLZLINWHATN-UHFFFAOYSA-N
SO4	C [auth A], D [auth A], E [auth A], M [auth B], N [auth B], O [auth B], P [auth B], Q [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], S [auth B], T [auth B], U [auth B], V [auth B], W [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.186 
• R-Value Work: 0.158 
• R-Value Observed: 0.159 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 139.095	α = 90
b = 139.095	β = 90
c = 151.654	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-2000	data scaling
HKL-3000	phasing
SHELX	phasing
MLPHARE	phasing
DM	phasing
RESOLVE	phasing
ARP/wARP	model building
O	model building
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-03-03 
• Released Date: 2006-04-25 
Deposition Author(s): Cuff, M.E., Skarina, T., Edwards, A., Savchenko, A., Cymborowski, M., Minor, W., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2006-04-25
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Source and taxonomy, Version format compliance
• Version 1.3: 2022-04-13
  Changes: Database references, Derived calculations, Structure summary