6GT8 | pdb_00006gt8

Sulfolobus solfataricus 2-keto-3-deoxygluconate aldolase Y132V,T157C variant

• PDB DOI: https://doi.org/10.2210/pdb6GT8/pdb

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


• Deposited: 2018-06-15 Released: 2019-06-26 
• 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: 3.15 Å
• R-Value Free: 
  0.236 (Depositor), 0.237 (DCC) 
• R-Value Work: 
  0.201 (Depositor), 0.201 (DCC) 
• R-Value Observed: 
  0.202 (Depositor) 

Starting Model: experimental

Literature

Sulfolobus solfataricus 2-keto-3-deoxygluconate aldolase Y132V,T157C 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: 66.42 kDa 
• Atom Count: 4,691 
• Modeled Residue Count: 588 
• Deposited Residue Count: 588 
• 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	293	Saccharolobus solfataricus	Mutation(s): 2  EC: 4.1.2.55
UniProt
Find proteins for O54288 (Saccharolobus solfataricus) Explore O54288  Go to UniProtKB:  O54288

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SSH	C [auth A], D [auth B]	3-DEOXY-D-ARABINO-HEXONIC ACID C6 H12 O6 YGMNHEPVTNXLLS-VAYJURFESA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
KPI	A, B	L-PEPTIDE LINKING	C9 H16 N2 O4		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.15 Å
• R-Value Free:  0.236 (Depositor), 0.237 (DCC) 
• R-Value Work:  0.201 (Depositor), 0.201 (DCC) 
• R-Value Observed: 0.202 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.08	α = 90
b = 103.08	β = 90
c = 243.392	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
Aimless	data scaling
BALBES	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-06-26 
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: 2019-06-26
  Type: Initial release
  
• Version 2.0: 2023-11-29
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Source and taxonomy
• Version 2.1: 2024-01-17
  Changes: Refinement description