1XI3

Thiamine phosphate pyrophosphorylase from Pyrococcus furiosus Pfu-1255191-001

• PDB DOI: https://doi.org/10.2210/pdb1XI3/pdb

• Classification: TRANSFERASE
• Organism(s): Pyrococcus furiosus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2004-09-21 Released: 2004-09-28 
• Deposition Author(s): Zhou, W., Chen, L., Tempel, W., Liu, Z.-J., Habel, J., Lee, D., Lin, D., Chang, S.-H., Dillard, B.D., Eneh, J.C., Hopkins, R.C., Jenney Jr., F.E., Kelley, L.-L.C., Lee, H.-S., Li, T., Poole II, F.L., Shah, C., Sugar, F.J., Arendall III, W.B., Richardson, J.S., Richardson, D.C., Rose, J.P., Adams, M.W.W., Wang, B.-C., Southeast Collaboratory for Structural Genomics (SECSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.215 
• R-Value Work: 0.188 
• R-Value Observed: 0.189 

Starting Model: experimental

Literature

Thiamine phosphate pyrophosphorylase from Pyrococcus furiosus Pfu-1255191-001

Zhou, W., Chen, L., Tempel, W., Liu, Z.-J., Habel, J., Lee, D., Lin, D., Chang, S.-H., DILLARD, B.D., Eneh, J.C., Hopkins, R.C., Jenney Jr., F.E., KELLEY, L.-L.C., Lee, H.-S., Li, T., Poole II, F.L., Shah, C., Sugar, F.J., Arendall III, W.B., Richardson, J.S., Richardson, D.C., Rose, J.P., Adams, M.W.W., Wang, B.-C., Southeast Collaboratory for Structural Genomics

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: 47.22 kDa 
• Atom Count: 3,322 
• Modelled Residue Count: 404 
• Deposited Residue Count: 430 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thiamine phosphate pyrophosphorylase	A, B	215	Pyrococcus furiosus	Mutation(s): 0  Gene Names: thiE EC: 2.5.1.3
UniProt
Find proteins for Q8U192 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)) Explore Q8U192  Go to UniProtKB:  Q8U192

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
NI	E [auth B]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N
UNX	D [auth A], F [auth B], G [auth B]	UNKNOWN ATOM OR ION X

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.215 
• R-Value Work: 0.188 
• R-Value Observed: 0.189 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.386	α = 90
b = 81.21	β = 90
c = 152.903	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-09-28 
Deposition Author(s): Zhou, W., Chen, L., Tempel, W., Liu, Z.-J., Habel, J., Lee, D., Lin, D., Chang, S.-H., Dillard, B.D., Eneh, J.C., Hopkins, R.C., Jenney Jr., F.E., Kelley, L.-L.C., Lee, H.-S., Li, T., Poole II, F.L., Shah, C., Sugar, F.J., Arendall III, W.B., Richardson, J.S., Richardson, D.C., Rose, J.P., Adams, M.W.W., Wang, B.-C., Southeast Collaboratory for Structural Genomics (SECSG)

Revision History  

• Version 1.0: 2004-09-28
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 1.4: 2023-08-23
  Changes: Data collection, Database references, Derived calculations, Refinement description