2BE3 | pdb_00002be3

Structure of a GTP Pyrophosphokinase Family Protein from Streptococcus pneumoniae

• PDB DOI: https://doi.org/10.2210/pdb2BE3/pdb

• Classification: TRANSFERASE
• Organism(s): Streptococcus pneumoniae TIGR4
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2005-10-21 Released: 2005-12-06 
• Deposition Author(s): Cuff, M.E., Hatzos, C., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.234 (Depositor), 0.233 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.181 (DCC) 
• R-Value Observed: 
  0.185 (Depositor) 

Literature

Structure of a GTP Pyrophosphokinase Family Protein from Streptococcus pneumoniae

Cuff, M.E., Hatzos, C., Joachimiak, A.

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.

Macromolecule Content 

• Total Structure Weight: 53.88 kDa 
• Atom Count: 3,557 
• Modeled Residue Count: 392 
• Deposited Residue Count: 452 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GTP pyrophosphokinase	A, B	226	Streptococcus pneumoniae TIGR4	Mutation(s): 6  Gene Names: SP1097 EC: 2.7.6.5
UniProt
Find proteins for A0A0H2UPY1 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)) Explore A0A0H2UPY1  Go to UniProtKB:  A0A0H2UPY1

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PG4	D [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
GOL	E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

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:  0.234 (Depositor), 0.233 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.181 (DCC) 
• R-Value Observed: 0.185 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.843	α = 90
b = 104.843	β = 90
c = 170.562	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
MAR345	data collection
HKL-2000	data scaling
HKL-3000	phasing
SHELXD	phasing
MLPHARE	phasing
DM	phasing
CCP4	phasing
RESOLVE	phasing
Coot	model building
O	model building
ARP/wARP	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-12-06 
Deposition Author(s): Cuff, M.E., Hatzos, C., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2005-12-06
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Source and taxonomy, Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary