6YR3

1.48 Angstrom Resolution Crystal Structure of Transaldolase from Thermoplasma acidophilum in complex with D-fructose 6-phosphate Schiff-base intermediate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.48 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.161 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Large-scale motions underlie physical but not chemical steps in transaldolase mechanism: Substrate binding by conformational selection and rate-determining product release

Sautner, V.Lietzow, T.H.Klaus, M.Funk, L.M.Tittmann, K.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Probable transaldolase
A, B, C, D, E
223Thermoplasma acidophilum DSM 1728Mutation(s): 0 
Gene Names: talTa0616
EC: 2.2.1.2
UniProt
Find proteins for Q9HKI3 (Thermoplasma acidophilum (strain ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165))
Explore Q9HKI3 
Go to UniProtKB:  Q9HKI3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9HKI3
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
F6R (Subject of Investigation/LOI)
Query on F6R

Download Ideal Coordinates CCD File 
F [auth A],
J [auth B],
M [auth C],
P [auth D],
R [auth E]
FRUCTOSE -6-PHOSPHATE
C6 H13 O9 P
GSXOAOHZAIYLCY-HSUXUTPPSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
G [auth A],
K [auth B],
N [auth C],
Q [auth D],
S [auth E]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT
Query on ACT

Download Ideal Coordinates CCD File 
H [auth A]
I [auth A]
L [auth B]
O [auth C]
T [auth E]
H [auth A],
I [auth A],
L [auth B],
O [auth C],
T [auth E],
U [auth E]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.48 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.161 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 148.51α = 90
b = 172.2β = 90
c = 100.58γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-04-28
    Type: Initial release
  • Version 1.1: 2024-01-24
    Changes: Data collection, Database references, Refinement description