4HO4 | pdb_00004ho4

Crystal structure of glucose 1-phosphate thymidylyltransferase from Aneurinibacillus thermoaerophilus complexed with thymidine and glucose-1-phosphate

• PDB DOI: https://doi.org/10.2210/pdb4HO4/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: 1.64 Å
• R-Value Free: 
  0.223 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.194 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of glucose 1-phosphate thymidylyltransferase from Aneurinibacillus thermoaerophilus complexed with thymidine and glucose-1-phosphate

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: 67.56 kDa 
• Atom Count: 5,183 
• Modelled Residue Count: 586 
• 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
G1P	C [auth A]	1-O-phosphono-alpha-D-glucopyranose C6 H13 O9 P HXXFSFRBOHSIMQ-VFUOTHLCSA-N
THM	D [auth A], E [auth A], H [auth B], I [auth B]	THYMIDINE C10 H14 N2 O5 IQFYYKKMVGJFEH-XLPZGREQSA-N
SO4	F [auth A], G [auth A], J [auth B], K [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.64 Å
• R-Value Free:  0.223 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.194 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.24	α = 90
b = 90.81	β = 125.05
c = 87.754	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: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Database references, Derived calculations, Structure summary
• Version 1.3: 2023-09-20
  Changes: Data collection, Database references, Refinement description, Structure summary