1T96 | pdb_00001t96

r106g kdo8ps with pep

• PDB DOI: https://doi.org/10.2210/pdb1T96/pdb

• Classification: TRANSFERASE
• Organism(s): Aquifex aeolicus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2004-05-14 Released: 2005-06-14 
• Deposition Author(s): Gatti, D.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.246 (Depositor), 0.245 (DCC) 
• R-Value Work: 
  0.204 (Depositor), 0.204 (DCC) 

Starting Model: experimental

Literature

Effects of the Arg106==>Gly mutation on the catalytic and conformational cycle of Aquifex aeolicus KDO8P synthase.

Xu, X., Wang, J., Kona, F., Divvela, P., Stemmler, T., Gatti, D.L.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 60.1 kDa 
• Atom Count: 4,536 
• Modeled Residue Count: 511 
• Deposited Residue Count: 534 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2-dehydro-3-deoxyphosphooctonate aldolase	A, B	267	Aquifex aeolicus	Mutation(s): 1  Gene Names: KDSA, AQ_085 EC: 2.5.1.55
UniProt
Find proteins for O66496 (Aquifex aeolicus (strain VF5)) Explore O66496  Go to UniProtKB:  O66496

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEP	E [auth A], H [auth B]	PHOSPHOENOLPYRUVATE C3 H5 O6 P DTBNBXWJWCWCIK-UHFFFAOYSA-N
CD	D [auth A], G [auth B]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N
PO4	C [auth A], F [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.246 (Depositor), 0.245 (DCC) 
• R-Value Work:  0.204 (Depositor), 0.204 (DCC) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.028	α = 90
b = 85.028	β = 90
c = 161.151	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
CrystalClear	data reduction
d*TREK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-06-14 
Deposition Author(s): Gatti, D.L.

Revision History  

• Version 1.0: 2005-06-14
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2011-11-16
  Changes: Atomic model
• Version 1.4: 2021-10-27
  Changes: Database references, Derived calculations
• Version 1.5: 2023-08-23
  Changes: Data collection, Refinement description