3NZR

Crystal structure of 2-dehydro-3-deoxyphosphogluconate aldolase from Vibrio fischeri ES114

• PDB DOI: https://doi.org/10.2210/pdb3NZR/pdb

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


• Deposited: 2010-07-16 Released: 2010-09-08 
• Deposition Author(s): Nocek, B., Marshall, N., Feldmann, B., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.225 
• R-Value Work: 0.174 
• R-Value Observed: 0.177 

Literature

Crystal structure of 2-dehydro-3-deoxyphosphogluconate aldolase from Vibrio fischeri ES114

Nocek, B., Marshall, N., Feldmann, B., 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)

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)

Macromolecule Content

• Total Structure Weight: 107.49 kDa 
• Atom Count: 8,011 
• Modelled Residue Count: 980 
• Deposited Residue Count: 992 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2-dehydro-3-deoxyphosphogluconate aldolase	A, B, C, D	248	Aliivibrio fischeri ES114	Mutation(s): 0  Gene Names: VF_2509 EC: 4.1.2.14 (PDB Primary Data), 4.1.3.16 (PDB Primary Data)
UniProt
Find proteins for Q5E1U2 (Aliivibrio fischeri (strain ATCC 700601 / ES114)) Explore Q5E1U2  Go to UniProtKB:  Q5E1U2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	E [auth A], F [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.225 
• R-Value Work: 0.174 
• R-Value Observed: 0.177 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.752	α = 90
b = 136.451	β = 101.38
c = 62.295	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-09-08 
Deposition Author(s): Nocek, B., Marshall, N., Feldmann, B., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2010-09-08
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance