3EGL | pdb_00003egl

Crystal Structure of DegV Family Protein Cg2579 from Corynebacterium glutamicum

• PDB DOI: https://doi.org/10.2210/pdb3EGL/pdb

• Classification: structural genomics, unknown function
• Organism(s): Corynebacterium glutamicum ATCC 13032
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-09-11 Released: 2008-09-23 
• Deposition Author(s): Kim, Y., Tesar, C., Abdullah, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.41 Å
• R-Value Free: 
  0.218 (Depositor), 0.224 (DCC) 
• R-Value Work: 
  0.179 (Depositor), 0.187 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Literature

Crystal Structure of DegV Family Protein Cg2579 from Corynebacterium glutamicum

Kim, Y., Tesar, C., Abdullah, J., Joachimiak, A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 90.72 kDa 
• Atom Count: 6,548 
• Modeled Residue Count: 793 
• Deposited Residue Count: 831 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DegV family protein	A, B, C	277	Corynebacterium glutamicum ATCC 13032	Mutation(s): 0  Gene Names: Cgl2349, cg2579
UniProt
Find proteins for Q8NN60 (Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / BCRC 11384 / CCUG 27702 / LMG 3730 / NBRC 12168 / NCIMB 10025 / NRRL B-2784 / 534)) Explore Q8NN60  Go to UniProtKB:  Q8NN60

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PLM	D [auth A], E [auth B], F [auth C]	PALMITIC ACID C16 H32 O2 IPCSVZSSVZVIGE-UHFFFAOYSA-N
FMT	G [auth C]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MLY	A, B, C	L-PEPTIDE LINKING	C8 H18 N2 O2		LYS
MSE	A, B, C	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.41 Å
• R-Value Free:  0.218 (Depositor), 0.224 (DCC) 
• R-Value Work:  0.179 (Depositor), 0.187 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.253	α = 90
b = 151.667	β = 90
c = 76.88	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	data collection
HKL-3000	phasing
MLPHARE	phasing
DM	model building
SHELXD	phasing
RESOLVE	model building
Coot	model building
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing
RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-09-23 
Deposition Author(s): Kim, Y., Tesar, C., Abdullah, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2008-09-23
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Refinement description, Source and taxonomy, Version format compliance
• Version 1.2: 2025-03-26
  Changes: Data collection, Database references, Derived calculations, Structure summary