3GDW | pdb_00003gdw

Crystal structure of sigma-54 interaction domain protein from Enterococcus faecalis

• PDB DOI: https://doi.org/10.2210/pdb3GDW/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Enterococcus faecalis V583
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-02-24 Released: 2009-03-10 
• Deposition Author(s): Chang, C., Sather, A., Buck, K., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.214 (Depositor), 0.218 (DCC) 
• R-Value Work: 
  0.183 (Depositor), 0.195 (DCC) 
• R-Value Observed: 
  0.185 (Depositor) 

Literature

Crystal structure of sigma-54 interaction domain protein from Enterococcus faecalis

Chang, C., Sather, A., Buck, K., Joachimiak, A.

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: 31.87 kDa 
• Atom Count: 2,403 
• Modeled Residue Count: 273 
• Deposited Residue Count: 278 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sigma-54 interaction domain protein	A, B	139	Enterococcus faecalis V583	Mutation(s): 0  Gene Names: EF_1010
UniProt
Find proteins for Q836U6 (Enterococcus faecalis (strain ATCC 700802 / V583)) Explore Q836U6  Go to UniProtKB:  Q836U6

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	C [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: 2.00 Å
• R-Value Free:  0.214 (Depositor), 0.218 (DCC) 
• R-Value Work:  0.183 (Depositor), 0.195 (DCC) 
• R-Value Observed: 0.185 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.127	α = 90
b = 71.418	β = 90
c = 94.502	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	phasing
MLPHARE	phasing
DM	model building
SHELXD	phasing
RESOLVE	model building
ARP/wARP	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: 2009-03-10 
Deposition Author(s): Chang, C., Sather, A., Buck, K., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2009-03-10
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Source and taxonomy, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary