2PT5 | pdb_00002pt5

Crystal Structure Of Shikimate Kinase (aq_2177) From Aquifex Aeolicus vf5

• PDB DOI: https://doi.org/10.2210/pdb2PT5/pdb

• Classification: TRANSFERASE
• Organism(s): Aquifex aeolicus VF5
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-05-08 Released: 2008-05-13 
• Deposition Author(s): Jeyakanthan, J., Nithya, N., Shimada, A., Velmurugan, D., Ebihara, A., Shinkai, A., Kuramitsu, S., Shiro, Y., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.269 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.214 (Depositor), 0.214 (DCC) 
• R-Value Observed: 
  0.214 (Depositor) 

Literature

Crystal Structure Of Shikimate Kinase (aq_2177) From Aquifex Aeolicus vf5

Jeyakanthan, J., Nithya, N., Shimada, A., Velmurugan, D., Ebihara, A., Shinkai, A., Kuramitsu, S., Shiro, Y., Yokoyama, S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors.

Biological Assembly 5  

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

Biological assembly 5 generated by PISA (software)

Biological Assembly 6  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 6 generated by PISA (software)

Biological Assembly 7  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 7 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 77.16 kDa 
• Atom Count: 5,453 
• Modeled Residue Count: 648 
• Deposited Residue Count: 672 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Shikimate kinase	A, B, C, D	168	Aquifex aeolicus VF5	Mutation(s): 0  Gene Names: aroK EC: 2.7.1.71
UniProt
Find proteins for O67925 (Aquifex aeolicus (strain VF5)) Explore O67925  Go to UniProtKB:  O67925

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	F [auth C]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO	E [auth C]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

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: 2.10 Å
• R-Value Free:  0.269 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.214 (Depositor), 0.214 (DCC) 
• R-Value Observed: 0.214 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.598	α = 90
b = 57.932	β = 90.59
c = 97.143	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-05-13 
Deposition Author(s): Jeyakanthan, J., Nithya, N., Shimada, A., Velmurugan, D., Ebihara, A., Shinkai, A., Kuramitsu, S., Shiro, Y., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2008-05-13
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary