3M6L | pdb_00003m6l

Crystal structure of transketolase in complex with thiamine diphosphate, ribose-5-phosphate and calcium ion

• PDB DOI: https://doi.org/10.2210/pdb3M6L/pdb

• Classification: TRANSFERASE
• Organism(s): Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-03-15 Released: 2010-04-28 
• Deposition Author(s): Nocek, B., Makowska-Grzyska, M., Maltseva, N., Joachimiak, A., Anderson, W., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.59 Å
• R-Value Free: 
  0.201 (Depositor), 0.204 (DCC) 
• R-Value Work: 
  0.160 (Depositor), 0.168 (DCC) 
• R-Value Observed: 
  0.162 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of transketolase in complex with thiamine diphosphate, ribose-5-phosphate and calcium ion

Nocek, B., Makowska-Grzyska, M., Maltseva, N., Grimshaw, S., Joachimiak, A., Anderson, W.

To be published.

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)

Macromolecule Content 

• Total Structure Weight: 71.37 kDa 
• Atom Count: 5,535 
• Modeled Residue Count: 632 
• Deposited Residue Count: 635 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transketolase	A	635	Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819	Mutation(s): 0  Gene Names: tkt, Cj1645 EC: 2.2.1.1
UniProt
Find proteins for Q0P7Y3 (Campylobacter jejuni subsp. jejuni serotype O:2 (strain ATCC 700819 / NCTC 11168)) Explore Q0P7Y3  Go to UniProtKB:  Q0P7Y3

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TPP	C [auth A]	THIAMINE DIPHOSPHATE C12 H19 N4 O7 P2 S AYEKOFBPNLCAJY-UHFFFAOYSA-O
R5P	F [auth A]	RIBOSE-5-PHOSPHATE C5 H11 O8 P PPQRONHOSHZGFQ-LMVFSUKVSA-N
PO4	G [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	B [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	E [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA	D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.59 Å
• R-Value Free:  0.201 (Depositor), 0.204 (DCC) 
• R-Value Work:  0.160 (Depositor), 0.168 (DCC) 
• R-Value Observed: 0.162 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m33m6l

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 130.924	α = 90
b = 71.462	β = 109.48
c = 69.617	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
MOLREP	phasing
Coot	model building
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-04-28 
Deposition Author(s): Nocek, B., Makowska-Grzyska, M., Maltseva, N., Joachimiak, A., Anderson, W., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2010-04-28
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2014-10-01
  Changes: Structure summary
• Version 1.3: 2017-11-08
  Changes: Advisory, Refinement description
• Version 1.4: 2023-09-06
  Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description
• Version 1.5: 2023-11-22
  Changes: Data collection
• Version 1.6: 2024-11-27
  Changes: Structure summary