6N0U | pdb_00006n0u

Crystal structure of a glucose-1-phosphate thymidylyltransferase from Burkholderia phymatum bound to 2'-deoxy-thymidine-B-L-rhamnose

• PDB DOI: https://doi.org/10.2210/pdb6N0U/pdb

• Classification: TRANSFERASE
• Organism(s): Paraburkholderia phymatum STM815
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-11-07 Released: 2018-11-21 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.233 (Depositor), 0.233 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.183 (DCC) 
• R-Value Observed: 
  0.185 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a glucose-1-phosphate thymidylyltransferase from Burkholderia phymatum bound to 2'-deoxy-thymidine-B-L-rhamnose

Edwards, T.E., Abendroth, J., Lorimer, D.D., Horanyi, P.S., Seattle Structural Genomics Center for Infectious Disease (SSGCID)

To be published.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 138.77 kDa 
• Atom Count: 9,576 
• Modeled Residue Count: 1,171 
• Deposited Residue Count: 1,220 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucose-1-phosphate thymidylyltransferase	A, B, C, D	305	Paraburkholderia phymatum STM815	Mutation(s): 0  Gene Names: Bphy_2318 EC: 2.7.7.24
UniProt
Find proteins for B2JFC5 (Paraburkholderia phymatum (strain DSM 17167 / CIP 108236 / LMG 21445 / STM815)) Explore B2JFC5  Go to UniProtKB:  B2JFC5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TRH	E [auth A], G [auth B], H [auth C], J [auth D]	2'-DEOXY-THYMIDINE-BETA-L-RHAMNOSE C16 H26 N2 O15 P2 ZOSQFDVXNQFKBY-CGAXJHMRSA-N
EDO	F [auth A], I [auth C]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.233 (Depositor), 0.233 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.183 (DCC) 
• R-Value Observed: 0.185 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m36n0u

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 152.32	α = 90
b = 80.18	β = 123.38
c = 131.04	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-11-21 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2018-11-21
  Type: Initial release
  
• Version 1.1: 2023-10-11
  Changes: Data collection, Database references, Refinement description