2YDA | pdb_00002yda

Sulfolobus sulfataricus 2-keto-3-deoxygluconate aldolase Y103F,Y130F, A198F variant

• PDB DOI: https://doi.org/10.2210/pdb2YDA/pdb

• Classification: LYASE
• Organism(s): Saccharolobus solfataricus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2011-03-18 Released: 2012-03-28 
• Deposition Author(s): Crennell, S.J., Royer, S.F., Angelopoulou, M., Hough, D.W., Danson, M.J., Bull, S.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.91 Å
• R-Value Free: 
  0.210 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.172 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.174 (Depositor) 

Starting Model: experimental

Literature

Sulfolobus Sulfataricus 2-Keto-3-Deoxygluconate Aldolase

Royer, S.F., Crennell, S.J., Angelopolou, M., Hough, D.W., Danson, M.J., Bull, S.D.

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 (software)

Macromolecule Content 

• Total Structure Weight: 67.21 kDa 
• Atom Count: 5,275 
• Modeled Residue Count: 585 
• Deposited Residue Count: 588 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2-KETO-3-DEOXY GLUCONATE ALDOLASE	A, B	294	Saccharolobus solfataricus	Mutation(s): 3  EC: 4.1.2.20 (PDB Primary Data), 4.1.2.55 (UniProt)
UniProt
Find proteins for O54288 (Saccharolobus solfataricus) Explore O54288  Go to UniProtKB:  O54288

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EPE	E [auth A]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N
GOL	C [auth A], D [auth A], F [auth B], G [auth B], H [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
IPA	I [auth B], J [auth B]	ISOPROPYL ALCOHOL C3 H8 O KFZMGEQAYNKOFK-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.91 Å
• R-Value Free:  0.210 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.172 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.174 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.62	α = 90
b = 99.62	β = 90
c = 249.01	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
BALBES	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-03-28 
Deposition Author(s): Crennell, S.J., Royer, S.F., Angelopoulou, M., Hough, D.W., Danson, M.J., Bull, S.D.

Revision History  

• Version 1.0: 2012-03-28
  Type: Initial release
  
• Version 1.1: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description
• Version 1.2: 2024-11-13
  Changes: Structure summary