6H2S | pdb_00006h2s

Sulfolobus solfataricus 2-keto-3-deoxygluconate aldolase T157V/D181Q/A198L variant, pyruvate complex

• PDB DOI: https://doi.org/10.2210/pdb6H2S/pdb

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


• Deposited: 2018-07-16 Released: 2019-07-31 
• Deposition Author(s): Crennell, S.J., Danson, M.J., Royer, S.
• Funding Organization(s): Biotechnology and Biological Sciences Research Council

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.17 Å
• R-Value Free: 
  0.196 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.145 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.148 (Depositor) 

Starting Model: experimental

Literature

Sulfolobus solfataricus 2-keto-3-deoxygluconate aldolase T157V/D181Q/A198L variant

Crennell, S.J., Danson, M.J., Royer, S.

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)

Biological Assembly Evidence: equilibrium centrifugation

Macromolecule Content 

• Total Structure Weight: 133.57 kDa 
• Atom Count: 10,292 
• Modeled Residue Count: 1,172 
• Deposited Residue Count: 1,172 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2-dehydro-3-deoxy-phosphogluconate/2-dehydro-3-deoxy-6-phosphogalactonate aldolase	A, B, C, D	293	Saccharolobus solfataricus	Mutation(s): 3  EC: 4.1.2.55
UniProt
Find proteins for Q97U28 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)) Explore Q97U28  Go to UniProtKB:  Q97U28

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	H [auth A], O [auth C]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL	F [auth A], G [auth A], K [auth B], L [auth B], N [auth C], Q [auth D], R [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
PYR	E [auth A], J [auth B], M [auth C], P [auth D]	PYRUVIC ACID C3 H4 O3 LCTONWCANYUPML-UHFFFAOYSA-N
IPA	I [auth A]	ISOPROPYL ALCOHOL C3 H8 O KFZMGEQAYNKOFK-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.17 Å
• R-Value Free:  0.196 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.145 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.148 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.56	α = 90
b = 87.016	β = 95.74
c = 92	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-07-31 
Deposition Author(s): Crennell, S.J., Danson, M.J., Royer, S.

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Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council	United Kingdom	--

Revision History  

• Version 1.0: 2019-07-31
  Type: Initial release
  
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection, Database references
• Version 2.1: 2024-01-17
  Changes: Refinement description
• Version 2.2: 2024-10-16
  Changes: Structure summary