6L19 | pdb_00006l19

The crystal structure of competence or damage-inducible protein from Enterobacter asburiae

• PDB DOI: https://doi.org/10.2210/pdb6L19/pdb

• Classification: HYDROLASE
• Organism(s): Enterobacter asburiae
• Expression System: Escherichia coli K-12
• Mutation(s): Yes 


• Deposited: 2019-09-28 Released: 2019-10-16 
• Deposition Author(s): Wang, L., Chen, Y., Liu, W., Lan, J., Shang, F., Xu, Y.
• Funding Organization(s): National Natural Science Foundation of China

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.13 Å
• R-Value Free: 
  0.221 (Depositor), 0.218 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.184 (DCC) 
• R-Value Observed: 
  0.188 (Depositor) 

Literature

The crystal structure of Competence or damage-inducible protein from Enterobacter asburiae

Wang, L., Chen, Y., Liu, W., Lan, J., Shang, F., Xu, Y.

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 Evidence: homology

Macromolecule Content 

• Total Structure Weight: 36.76 kDa 
• Atom Count: 2,646 
• Modeled Residue Count: 323 
• Deposited Residue Count: 344 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PncC family amidohydrolase	A, B	172	Enterobacter asburiae	Mutation(s): 3  Gene Names: DFS27_0727

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL (Subject of Investigation/LOI)	E [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL (Subject of Investigation/LOI)	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA (Subject of Investigation/LOI)	D [auth A], F [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.13 Å
• R-Value Free:  0.221 (Depositor), 0.218 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.184 (DCC) 
• R-Value Observed: 0.188 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 128.915	α = 90
b = 128.915	β = 90
c = 56.277	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-10-16 
Deposition Author(s): Wang, L., Chen, Y., Liu, W., Lan, J., Shang, F., Xu, Y.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	31200556
National Natural Science Foundation of China	China	21272031

Revision History  

• Version 1.0: 2019-10-16
  Type: Initial release
  
• Version 1.1: 2024-03-27
  Changes: Data collection, Database references