2Q5R

Structure of apo Staphylococcus aureus D-tagatose-6-phosphate kinase

• PDB DOI: https://doi.org/10.2210/pdb2Q5R/pdb

• Classification: TRANSFERASE
• Organism(s): Staphylococcus aureus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2007-06-01 Released: 2007-06-12 
• Deposition Author(s): McGrath, T.E., Soloveychik, M., Romanov, V., Thambipillai, D., Dharamsi, A., Virag, C., Domagala, M., Pai, E.F., Edwards, A.M., Battaile, K., Chirgadze, N.Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.283 
• R-Value Work: 0.215 
• R-Value Observed: 0.218 

Literature

Structure of apo Staphylococcus aureus D-tagatose-6-phosphate kinase

McGrath, T.E., Soloveychik, M., Romanov, V., Thambipillai, D., Dharamsi, A., Virag, C., Domagala, M., Pai, E.F., Edwards, A.M., Battaile, K., Chirgadze, N.Y.

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)

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: 144.78 kDa 
• Atom Count: 10,117 
• Modelled Residue Count: 1,243 
• Deposited Residue Count: 1,320 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tagatose-6-phosphate kinase	A, B, C, D	330	Staphylococcus aureus	Mutation(s): 2  Gene Names: lacC EC: 2.7.1.144
UniProt
Find proteins for Q5HE12 (Staphylococcus aureus (strain COL)) Explore Q5HE12  Go to UniProtKB:  Q5HE12

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.283 
• R-Value Work: 0.215 
• R-Value Observed: 0.218 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.952	α = 90
b = 96.94	β = 94.42
c = 94.485	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
JDirector	data collection
HKL-2000	data reduction
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-06-12 
Deposition Author(s): McGrath, T.E., Soloveychik, M., Romanov, V., Thambipillai, D., Dharamsi, A., Virag, C., Domagala, M., Pai, E.F., Edwards, A.M., Battaile, K., Chirgadze, N.Y.

Revision History  

• Version 1.0: 2007-06-12
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.5: 2023-11-15
  Changes: Data collection