3E9A | pdb_00003e9a

Crystal structure of 2-dehydro-3-deoxyphosphooctonate aldolase from Vibrio cholerae O1 biovar eltor str. N16961

• PDB DOI: https://doi.org/10.2210/pdb3E9A/pdb

• Classification: TRANSFERASE
• Organism(s): Vibrio cholerae O1 biovar El Tor
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-08-21 Released: 2008-09-16 
• Deposition Author(s): Nocek, B., Mulligan, R., Kwon, K., Joachimiak, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.215 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.176 (Depositor), 0.181 (DCC) 
• R-Value Observed: 
  0.178 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of 2-dehydro-3-deoxyphosphooctonate aldolase from Vibrio cholerae O1 biovar eltor str. N16961

Nocek, B., Mulligan, R., Kwon, K., Joachimiak, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 31.18 kDa 
• Atom Count: 2,296 
• Modeled Residue Count: 275 
• Deposited Residue Count: 286 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2-dehydro-3-deoxyphosphooctonate aldolase	A	286	Vibrio cholerae O1 biovar El Tor	Mutation(s): 0  Gene Names: kdsA, VC_2175 EC: 2.5.1.55
UniProt
Find proteins for A5F692 (Vibrio cholerae serotype O1 (strain ATCC 39541 / Classical Ogawa 395 / O395)) Explore A5F692  Go to UniProtKB:  A5F692

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.215 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.176 (Depositor), 0.181 (DCC) 
• R-Value Observed: 0.178 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m33e9a

Space Group: I 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.187	α = 90
b = 117.187	β = 90
c = 117.187	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
MOLREP	phasing
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-09-16 
Deposition Author(s): Nocek, B., Mulligan, R., Kwon, K., Joachimiak, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2008-09-16
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description