3URH | pdb_00003urh

Crystal structure of a dihydrolipoamide dehydrogenase from Sinorhizobium meliloti 1021

• PDB DOI: https://doi.org/10.2210/pdb3URH/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Sinorhizobium meliloti 1021
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-11-22 Released: 2011-12-14 
• Deposition Author(s): Kumaran, D., Chamala, S., Evans, B., Foti, R., Gizzi, A., Hillerich, B., Kar, A., LaFleur, J., Seidel, R., Villigas, G., Zencheck, W., Almo, S.C., Swaminathan, S., New York Structural Genomics Research Consortium (NYSGRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.227 (Depositor), 0.233 (DCC) 
• R-Value Work: 
  0.184 (Depositor), 0.192 (DCC) 
• R-Value Observed: 
  0.186 (Depositor) 

Literature

Crystal structure of a dihydrolipoamide dehydrogenase from Sinorhizobium meliloti 1021

Kumaran, D., Almo, S.C., Swaminathan, S.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 106.35 kDa 
• Atom Count: 7,292 
• Modeled Residue Count: 926 
• Deposited Residue Count: 982 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydrolipoyl dehydrogenase	A, B	491	Sinorhizobium meliloti 1021	Mutation(s): 0  Gene Names: lpdA2, R03048, SMc02487 EC: 1.8.1.4
UniProt
Find proteins for Q92LK0 (Rhizobium meliloti (strain 1021)) Explore Q92LK0  Go to UniProtKB:  Q92LK0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	C [auth A], E [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
SO4	D [auth A], F [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	G [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: 1.90 Å
• R-Value Free:  0.227 (Depositor), 0.233 (DCC) 
• R-Value Work:  0.184 (Depositor), 0.192 (DCC) 
• R-Value Observed: 0.186 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.433	α = 90
b = 104.716	β = 90
c = 120.622	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
SHELXD	phasing
SHELXE	model building
ARP/wARP	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-12-14 
Deposition Author(s): Kumaran, D., Chamala, S., Evans, B., Foti, R., Gizzi, A., Hillerich, B., Kar, A., LaFleur, J., Seidel, R., Villigas, G., Zencheck, W., Almo, S.C., Swaminathan, S., New York Structural Genomics Research Consortium (NYSGRC)

Revision History  

• Version 1.0: 2011-12-14
  Type: Initial release
  
• Version 1.1: 2024-10-16
  Changes: Data collection, Database references, Derived calculations, Structure summary