2GGQ | pdb_00002ggq

complex of hypothetical glucose-1-phosphate thymidylyltransferase from sulfolobus tokodaii

• PDB DOI: https://doi.org/10.2210/pdb2GGQ/pdb

• Classification: TRANSFERASE
• Organism(s): Sulfurisphaera tokodaii
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2006-03-24 Released: 2007-03-24 
• Deposition Author(s): Rajakannan, V., Mizushima, T., Suzuki, A., Masui, R., Kuramitsu, S., Yamane, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.252 (Depositor), 0.249 (DCC) 
• R-Value Work: 
  0.191 (Depositor), 0.189 (DCC) 
• R-Value Observed: 
  0.194 (Depositor) 

Starting Model: experimental

Literature

complex of hypothetical glucose-1-phosphate thymidylyltransferase from sulfolobus tokodaii

Rajakannan, V., Yamane, T.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 generated by PISA,PQS (software)

Macromolecule Content 

• Total Structure Weight: 45.44 kDa 
• Atom Count: 3,370 
• Modeled Residue Count: 401 
• Deposited Residue Count: 401 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
401aa long hypothetical glucose-1-phosphate thymidylyltransferase	A	401	Sulfurisphaera tokodaii	Mutation(s): 0  EC: 2.7.7.24
UniProt
Find proteins for Q975F9 (Sulfurisphaera tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7)) Explore Q975F9  Go to UniProtKB:  Q975F9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TTP	E [auth A]	THYMIDINE-5'-TRIPHOSPHATE C10 H17 N2 O14 P3 NHVNXKFIZYSCEB-XLPZGREQSA-N
IOD	B [auth A], C [auth A], D [auth A]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.252 (Depositor), 0.249 (DCC) 
• R-Value Work:  0.191 (Depositor), 0.189 (DCC) 
• R-Value Observed: 0.194 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 122.75	α = 90
b = 122.75	β = 90
c = 95.518	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
ADSC	data collection
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-03-24 
Deposition Author(s): Rajakannan, V., Mizushima, T., Suzuki, A., Masui, R., Kuramitsu, S., Yamane, T.

Revision History  

• Version 1.0: 2007-03-24
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-10-23
  Changes: Structure summary