2YW3 | pdb_00002yw3

Crystal Structure Analysis of the 4-hydroxy-2-oxoglutarate aldolase/2-deydro-3-deoxyphosphogluconate aldolase from TTHB1

• PDB DOI: https://doi.org/10.2210/pdb2YW3/pdb

• Classification: LYASE
• Organism(s): Thermus thermophilus HB8
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-04-19 Released: 2007-10-23 
• Deposition Author(s): Kawano, Y., Hashimoto, K., Kamiya, N., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.67 Å
• R-Value Free: 
  0.214 (Depositor) 
• R-Value Work: 
  0.182 (Depositor) 
• R-Value Observed: 
  0.185 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure Analysis of the 4-hydroxy-2-oxoglutarate aldolase/2-deydro-3-deoxyphosphogluconate aldolase from TTHB1

Kawano, Y., Hashimoto, K., Kamiya, N.

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,PQS (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 2 assigned by authors and generated by PISA,PQS (software)

Macromolecule Content 

• Total Structure Weight: 132.09 kDa 
• Atom Count: 10,084 
• Modeled Residue Count: 1,187 
• Deposited Residue Count: 1,242 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
4-hydroxy-2-oxoglutarate aldolase/2-deydro-3-deoxyphosphogluconate aldolase	A, B, C, D, E, F	207	Thermus thermophilus HB8	Mutation(s): 0  EC: 4.1.2.14
UniProt
Find proteins for Q53W90 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q53W90  Go to UniProtKB:  Q53W90

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	G [auth A], H [auth B], I [auth B], J [auth B], K [auth C], L [auth D], M [auth D], N [auth D], O [auth D], P [auth E], Q [auth E], R [auth E], S [auth E], T [auth F], U [auth F], V [auth F], W [auth F]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.67 Å
• R-Value Free:  0.214 (Depositor) 
• R-Value Work:  0.182 (Depositor) 
• R-Value Observed: 0.185 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 125.922	α = 90
b = 72.685	β = 91.07
c = 161.312	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Rapid	data collection
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-10-23 
Deposition Author(s): Kawano, Y., Hashimoto, K., Kamiya, N., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2007-10-23
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Derived calculations, Source and taxonomy, Version format compliance
• Version 1.2: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description