5XQA

Crystal Structure of Transketolase in complex with ribose-5-phosphate from Pichia Stipitis

• PDB DOI: https://doi.org/10.2210/pdb5XQA/pdb

• Classification: TRANSFERASE
• Organism(s): Scheffersomyces stipitis CBS 6054
• Expression System: Escherichia coli K-12
• Mutation(s): No 


• Deposited: 2017-06-06 Released: 2018-06-06 
• Deposition Author(s): Li, T.L., Hsu, N.S., Wang, Y.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.14 Å
• R-Value Free: 0.141 
• R-Value Work: 0.129 
• R-Value Observed: 0.130 

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 75.75 kDa 
• Atom Count: 6,322 
• Modelled Residue Count: 675 
• Deposited Residue Count: 697 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transketolase	A	697	Scheffersomyces stipitis CBS 6054	Mutation(s): 0  Gene Names: TKT, TKT1, PICST_67105 EC: 2.2.1.1
UniProt
Find proteins for P34736 (Scheffersomyces stipitis (strain ATCC 58785 / CBS 6054 / NBRC 10063 / NRRL Y-11545)) Explore P34736  Go to UniProtKB:  P34736

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TPP	B [auth A]	THIAMINE DIPHOSPHATE C12 H19 N4 O7 P2 S AYEKOFBPNLCAJY-UHFFFAOYSA-O
HSX	D [auth A]	5-O-phosphono-alpha-D-ribofuranose C5 H11 O8 P KTVPXOYAKDPRHY-AIHAYLRMSA-N
CA	C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.14 Å
• R-Value Free: 0.141 
• R-Value Work: 0.129 
• R-Value Observed: 0.130 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.093	α = 90
b = 184.78	β = 90
c = 99.015	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data processing
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-06-06 
Deposition Author(s): Li, T.L., Hsu, N.S., Wang, Y.L.

Revision History  

• Version 1.0: 2018-06-06
  Type: Initial release
  
• Version 1.1: 2018-12-19
  Changes: Data collection, Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations
• Version 2.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description, Structure summary