6OVI | pdb_00006ovi

Crystal Structure of KDPG Aldolase from Legionella Pneumophila with pyruvate captured at low pH as a covalent carbinolamine intermediate

• PDB DOI: https://doi.org/10.2210/pdb6OVI/pdb

• Classification: LYASE
• Organism(s): Legionella pneumophila
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-05-07 Released: 2019-06-26 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)
• 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: 1.60 Å
• R-Value Free: 
  0.180 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.157 (Depositor), 0.158 (DCC) 
• R-Value Observed: 
  0.159 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of KDPG Aldolase from Legionella Pneumophila with pyruvate captured at low pH as a covalent carbinolamine intermediate

Davies, D.R., Dranow, D.M.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Macromolecule Content 

• Total Structure Weight: 74.46 kDa 
• Atom Count: 5,317 
• Modeled Residue Count: 625 
• Deposited Residue Count: 684 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Keto-deoxy-phosphogluconate aldolase	A, B, C	228	Legionella pneumophila	Mutation(s): 0  Gene Names: C3927_01390 EC: 4.1.2.14 (PDB Primary Data), 4.1.3.16 (PDB Primary Data)
UniProt
Find proteins for Q5ZYF2 (Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513)) Explore Q5ZYF2  Go to UniProtKB:  Q5ZYF2

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PVO (Subject of Investigation/LOI)	D [auth A], I [auth B], M [auth C]	2,2-bis(oxidanyl)propanoic acid C3 H6 O4 HPQUMJNDQVOTAZ-UHFFFAOYSA-N
SO4	F [auth A], G [auth A], H [auth A], L [auth B], O [auth C], P [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	E [auth A], J [auth B], K [auth B], N [auth C]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.180 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.157 (Depositor), 0.158 (DCC) 
• R-Value Observed: 0.159 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m36ovi

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.42	α = 90
b = 79.14	β = 117.4
c = 70.06	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-06-26 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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

Revision History  

• Version 1.0: 2019-06-26
  Type: Initial release
  
• Version 1.1: 2019-12-18
  Changes: Author supporting evidence
• Version 1.2: 2023-10-11
  Changes: Data collection, Database references, Refinement description
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection, Derived calculations