4HO9 | pdb_00004ho9

Crystal structure of glucose 1-phosphate thymidylyltransferase from Aneurinibacillus thermoaerophilus complexed with UDP-galactose and UTP

• PDB DOI: https://doi.org/10.2210/pdb4HO9/pdb

• Classification: TRANSFERASE
• Organism(s): Aneurinibacillus thermoaerophilus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-10-22 Released: 2013-10-23 
• Deposition Author(s): Chen, T.J., Chien, W.T., Lin, C.C., Wang, W.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.211 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.171 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.173 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of glucose 1-phosphate thymidylyltransferase from Aneurinibacillus thermoaerophilus complexed with UDP-galactose and UTP

Chen, T.J., Chien, W.T., Lin, C.C., Wang, W.C.

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: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 68.91 kDa 
• Atom Count: 5,253 
• Modeled Residue Count: 582 
• Deposited Residue Count: 594 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucose-1-phosphate thymidylyltransferase	A, B	297	Aneurinibacillus thermoaerophilus	Mutation(s): 0  Gene Names: rmlA EC: 2.7.7.24
UniProt
Find proteins for Q9AGY4 (Aneurinibacillus thermoaerophilus) Explore Q9AGY4  Go to UniProtKB:  Q9AGY4

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GDU	C [auth A], J [auth B]	GALACTOSE-URIDINE-5'-DIPHOSPHATE C15 H24 N2 O17 P2 HSCJRCZFDFQWRP-ABVWGUQPSA-N
UTP	D [auth A], K [auth B]	URIDINE 5'-TRIPHOSPHATE C9 H15 N2 O15 P3 PGAVKCOVUIYSFO-XVFCMESISA-N
SO4	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], L [auth B], M [auth B], N [auth B], O [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.211 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.171 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.173 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.788	α = 90
b = 90.763	β = 125.2
c = 87.702	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-10-23 
Deposition Author(s): Chen, T.J., Chien, W.T., Lin, C.C., Wang, W.C.

Revision History  

• Version 1.0: 2013-10-23
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Refinement description
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description