3L8M | pdb_00003l8m

Crystal Structure of a probable thiamine pyrophosphokinase from Staphylococcus saprophyticus subsp. saprophyticus. Northeast Structural Genomics Consortium target id SyR86

• PDB DOI: https://doi.org/10.2210/pdb3L8M/pdb

• Classification: TRANSFERASE
• Organism(s): Staphylococcus saprophyticus subsp. saprophyticus ATCC 15305 = NCTC 7292
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-12-31 Released: 2010-02-09 
• Deposition Author(s): Seetharaman, J., Lew, S., Wang, D., Janjua, H., Cunningham, K., Owens, L., Xiao, R., Liu, J., Baran, M.C., Acton, T.B., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.271 (Depositor), 0.279 (DCC) 
• R-Value Work: 
  0.238 (Depositor), 0.257 (DCC) 
• R-Value Observed: 
  0.238 (Depositor) 

Literature

Crystal Structure of a probable thiamine pyrophosphokinase from Staphylococcus saprophyticus subsp. saprophyticus. Northeast Structural Genomics Consortium target id SyR86

Seetharaman, J., Lew, S., Wang, D., Janjua, H., Cunningham, K., Owens, L., Xiao, R., Liu, J., Baran, M.C., Acton, T.B., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 48.52 kDa 
• Atom Count: 2,904 
• Modeled Residue Count: 370 
• Deposited Residue Count: 424 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
probable thiamine pyrophosphokinase	A, B	212	Staphylococcus saprophyticus subsp. saprophyticus ATCC 15305 = NCTC 7292	Mutation(s): 0  Gene Names: SSP1549 EC: 2.7.6.2
UniProt
Find proteins for Q49X04 (Staphylococcus saprophyticus subsp. saprophyticus (strain ATCC 15305 / DSM 20229 / NCIMB 8711 / NCTC 7292 / S-41)) Explore Q49X04  Go to UniProtKB:  Q49X04

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NA	C [auth A], D [auth A], E [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.271 (Depositor), 0.279 (DCC) 
• R-Value Work:  0.238 (Depositor), 0.257 (DCC) 
• R-Value Observed: 0.238 (Depositor) 

Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.873	α = 90
b = 101.873	β = 90
c = 88.024	γ = 120

Software Package:

Software Name	Purpose
ADSC	data collection
SHELXS	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-02-09 
Deposition Author(s): Seetharaman, J., Lew, S., Wang, D., Janjua, H., Cunningham, K., Owens, L., Xiao, R., Liu, J., Baran, M.C., Acton, T.B., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

Revision History  

• Version 1.0: 2010-02-09
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary