3VAA | pdb_00003vaa

1.7 Angstrom Resolution Crystal Structure of Shikimate Kinase from Bacteroides thetaiotaomicron

• PDB DOI: https://doi.org/10.2210/pdb3VAA/pdb

• Classification: TRANSFERASE
• Organism(s): Bacteroides thetaiotaomicron
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2011-12-29 Released: 2012-01-18 
• Deposition Author(s): Minasov, G., Light, S.H., Halavaty, A., Shuvalova, L., Papazisi, L., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.199 (Depositor), 0.202 (DCC) 
• R-Value Work: 
  0.163 (Depositor), 0.172 (DCC) 
• R-Value Observed: 
  0.165 (Depositor) 

Starting Model: experimental

Literature

1.7 Angstrom Resolution Crystal Structure of Shikimate Kinase from Bacteroides thetaiotaomicron.

Minasov, G., Light, S.H., Halavaty, A., Shuvalova, L., Papazisi, L., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

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

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

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 70.53 kDa 
• Atom Count: 4,945 
• Modeled Residue Count: 521 
• Deposited Residue Count: 597 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Shikimate kinase	A, B, C	199	Bacteroides thetaiotaomicron	Mutation(s): 0  Gene Names: aroK, BT_3393 EC: 2.7.1.71
UniProt
Find proteins for Q8A2B2 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50)) Explore Q8A2B2  Go to UniProtKB:  Q8A2B2

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	F [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4	K [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	E [auth A], H [auth B], I [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
BME	D [auth A], G [auth B], J [auth C]	BETA-MERCAPTOETHANOL C2 H6 O S DGVVWUTYPXICAM-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.199 (Depositor), 0.202 (DCC) 
• R-Value Work:  0.163 (Depositor), 0.172 (DCC) 
• R-Value Observed: 0.165 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m33vaa

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.253	α = 90
b = 46.46	β = 97.42
c = 105.124	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
BALBES	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-01-18 
Deposition Author(s): Minasov, G., Light, S.H., Halavaty, A., Shuvalova, L., Papazisi, L., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2012-01-18
  Type: Initial release
  
• Version 1.1: 2017-11-08
  Changes: Refinement description
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description