4BK9 | pdb_00004bk9

Crystal structure of 2-keto-3-deoxy-6-phospho-gluconate aldolase from Zymomonas mobilis ATCC 29191

• PDB DOI: https://doi.org/10.2210/pdb4BK9/pdb

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


• Deposited: 2013-04-22 Released: 2014-04-30 
• Deposition Author(s): Classen, T., Schlieper, D., Groth, G., Pietruszka, J.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.77 Å
• R-Value Free: 
  0.172 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.135 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.137 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of 2-Keto-3-Deoxy-6-Phospho- Gluconate Aldolase from Zymomonas Mobilis

Classen, T., Schlieper, D., Groth, G., Pietruszka, J.

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: 68.48 kDa 
• Atom Count: 4,617 
• Modeled Residue Count: 620 
• Deposited Residue Count: 648 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2-DEHYDRO-3-DEOXYPHOSPHOGLUCONATE ALDOLASE/4-HYDROXY-2-OXO GLUTARATE ALDOLASE	A, B, C	216	Zymomonas mobilis	Mutation(s): 0  EC: 4.1.2.14

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	D [auth A], E [auth A], F [auth B], G [auth B], H [auth B], I [auth B], J [auth C], K [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.77 Å
• R-Value Free:  0.172 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.135 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.137 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.38	α = 90
b = 118.05	β = 109.51
c = 55.91	γ = 90

Software Package:

Software Name	Purpose
REFMAC	model building
XPREP	data scaling
MrBUMP	phasing
CHAINSAW	phasing
PHASER	phasing
REFMAC	phasing
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-04-30 
Deposition Author(s): Classen, T., Schlieper, D., Groth, G., Pietruszka, J.

Revision History  

• Version 1.0: 2014-04-30
  Type: Initial release
  
• Version 1.1: 2019-05-08
  Changes: Data collection, Experimental preparation, Other
• Version 1.2: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description