5CD2 | pdb_00005cd2

The crystal structure of endo-1,4-D-glucanase from Vibrio fischeri ES114

• PDB DOI: https://doi.org/10.2210/pdb5CD2/pdb

• Classification: HYDROLASE
• Organism(s): Aliivibrio fischeri ES114
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-07-02 Released: 2015-07-22 
• Deposition Author(s): Tan, K., Li, H., Endres, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 
  0.176 (Depositor) 
• R-Value Work: 
  0.135 (Depositor) 
• R-Value Observed: 
  0.137 (Depositor) 

Literature

The crystal structure of endo-1,4-D-glucanase from Vibrio fischeri ES114

Tan, K., Li, H., Endres, M., Joachimiak, A.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 42.4 kDa 
• Atom Count: 3,227 
• Modeled Residue Count: 345 
• Deposited Residue Count: 372 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endo-1,4-D-glucanase	A	372	Aliivibrio fischeri ES114	Mutation(s): 0  Gene Names: bcsZ, VF_A0882 EC: 3.2.1.4
UniProt
Find proteins for Q5DZ44 (Aliivibrio fischeri (strain ATCC 700601 / ES114)) Explore Q5DZ44  Go to UniProtKB:  Q5DZ44

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	B [auth A], C [auth A], D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
NI	F [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N
CL	E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free:  0.176 (Depositor) 
• R-Value Work:  0.135 (Depositor) 
• R-Value Observed: 0.137 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.563	α = 90
b = 67.489	β = 90
c = 101.192	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2015-07-22 
Deposition Author(s): Tan, K., Li, H., Endres, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM102318

Revision History  

• Version 1.0: 2015-07-22
  Type: Initial release
  
• Version 1.1: 2017-09-06
  Changes: Author supporting evidence, Derived calculations, Source and taxonomy
• Version 1.2: 2019-12-25
  Changes: Author supporting evidence
• Version 1.3: 2024-11-13
  Changes: Data collection, Database references, Derived calculations, Structure summary