5XSF | pdb_00005xsf

Crystal structure of the 2-keto-3-deoxy-6-phosphogluconate aldolase of Zymomonas mobilis ZM4 with 3-phosphoglycerate

• PDB DOI: https://doi.org/10.2210/pdb5XSF/pdb

• Classification: LYASE
• Organism(s): Zymomonas mobilis subsp. mobilis ZM4 = ATCC 31821
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-06-14 Released: 2018-06-20 
• Deposition Author(s): Seo, P.W., Kim, J.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.96 Å
• R-Value Free: 
  0.212 (Depositor), 0.213 (DCC) 
• R-Value Work: 
  0.191 (Depositor), 0.194 (DCC) 
• R-Value Observed: 
  0.192 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the 2-keto-3-deoxy-6-phosphogluconate aldolase of Zymomonas mobilis ZM4

Seo, P.W., Kim, J.S.

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: 22.08 kDa 
• Atom Count: 1,709 
• Modeled Residue Count: 209 
• Deposited Residue Count: 209 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
KHG/KDPG aldolase	A	209	Zymomonas mobilis subsp. mobilis ZM4 = ATCC 31821	Mutation(s): 0  Gene Names: eda, kdgA, ZMO0997 EC: 4.1.2.14
UniProt
Find proteins for Q00384 (Zymomonas mobilis subsp. mobilis (strain ATCC 31821 / ZM4 / CP4)) Explore Q00384  Go to UniProtKB:  Q00384

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
3PG (Subject of Investigation/LOI)	D [auth A]	3-PHOSPHOGLYCERIC ACID C3 H7 O7 P OSJPPGNTCRNQQC-UWTATZPHSA-N
3PY (Subject of Investigation/LOI)	E [auth A]	3-HYDROXYPYRUVIC ACID C3 H4 O4 HHDDCCUIIUWNGJ-UHFFFAOYSA-N
PO4 (Subject of Investigation/LOI)	B [auth A], C [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.96 Å
• R-Value Free:  0.212 (Depositor), 0.213 (DCC) 
• R-Value Work:  0.191 (Depositor), 0.194 (DCC) 
• R-Value Observed: 0.192 (Depositor) 

Space Group: F 4₁ 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 186.299	α = 90
b = 186.299	β = 90
c = 186.299	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-06-20 
Deposition Author(s): Seo, P.W., Kim, J.S.

Revision History  

• Version 1.0: 2018-06-20
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description