5VU3 | pdb_00005vu3

Crystal structure of the competence-damaged protein (CinA) superfamily protein ECL_02051 from Enterobacter cloacae

• PDB DOI: https://doi.org/10.2210/pdb5VU3/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Enterobacter cloacae subsp. cloacae ATCC 13047
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-05-18 Released: 2017-06-14 
• Deposition Author(s): Stogios, P.J., Skarina, T., McChesney, C., Sandoval, J., Di Leo, R., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.87 Å
• R-Value Free: 
  0.193 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.151 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.152 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the competence-damaged protein (CinA) superfamily protein ECL_02051 from Enterobacter cloacae

Stogios, P.J.

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)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 142.7 kDa 
• Atom Count: 11,834 
• Modeled Residue Count: 1,344 
• Deposited Residue Count: 1,360 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Competence damage-inducible protein A	A, B, C, D, E, F, G, H	170	Enterobacter cloacae subsp. cloacae ATCC 13047	Mutation(s): 0  Gene Names: cinA, ECL_02051
UniProt
Find proteins for A0A0H3CM13 (Enterobacter cloacae subsp. cloacae (strain ATCC 13047 / DSM 30054 / NBRC 13535 / NCTC 10005 / WDCM 00083 / NCDC 279-56)) Explore A0A0H3CM13  Go to UniProtKB:  A0A0H3CM13

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PG4	J [auth G]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
ACT	I [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.87 Å
• R-Value Free:  0.193 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.151 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.152 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.529	α = 85.27
b = 52.825	β = 87.19
c = 132.156	γ = 68.98

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing
PHENIX	model building
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-06-14 
Deposition Author(s): Stogios, P.J., Skarina, T., McChesney, C., Sandoval, J., Di Leo, R., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	HHSN272201200026C

Revision History  

• Version 1.0: 2017-06-14
  Type: Initial release
  
• Version 1.1: 2017-09-20
  Changes: Author supporting evidence
• Version 1.2: 2019-12-11
  Changes: Author supporting evidence
• Version 1.3: 2023-10-04
  Changes: Data collection, Database references, Refinement description