3BAF | pdb_00003baf

Crystal structure of shikimate kinase from Mycobacterium tuberculosis in complex with AMP-PNP

• PDB DOI: https://doi.org/10.2210/pdb3BAF/pdb

• Classification: TRANSFERASE
• Organism(s): Mycobacterium tuberculosis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-11-07 Released: 2008-11-11 
• Deposition Author(s): Faim, L.M., Dias, M.V.B., Vasconcelos, I.G., Basso, L.A., Santos, D.S., Azevedo, W.F., Ruggiero, N.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 
  0.284 (Depositor), 0.271 (DCC) 
• R-Value Work: 
  0.207 (Depositor) 
• R-Value Observed: 
  0.210 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure for shikimate kinase from Mycobacterium tuberculosis in complex with AMP-PNP

Faim, L.M., Dias, M.V.B., Vasconcelos, I.G., Basso, L.A., Santos, D.S., Azevedo, W.F., Ruggiero, N.J.

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)

Macromolecule Content 

• Total Structure Weight: 19.29 kDa 
• Atom Count: 1,405 
• Modeled Residue Count: 165 
• Deposited Residue Count: 176 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Shikimate kinase	A	176	Mycobacterium tuberculosis	Mutation(s): 0  Gene Names: aroK EC: 2.7.1.71
UniProt
Find proteins for P9WPY3 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WPY3  Go to UniProtKB:  P9WPY3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ANP	B [auth A]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C10 H17 N6 O12 P3 PVKSNHVPLWYQGJ-KQYNXXCUSA-N
SKM	C [auth A]	(3R,4S,5R)-3,4,5-TRIHYDROXYCYCLOHEX-1-ENE-1-CARBOXYLIC ACID C7 H10 O5 JXOHGGNKMLTUBP-HSUXUTPPSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free:  0.284 (Depositor), 0.271 (DCC) 
• R-Value Work:  0.207 (Depositor) 
• R-Value Observed: 0.210 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.297	α = 90
b = 67.297	β = 90
c = 97.692	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
MAR345dtb	data collection
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-11-11 
Deposition Author(s): Faim, L.M., Dias, M.V.B., Vasconcelos, I.G., Basso, L.A., Santos, D.S., Azevedo, W.F., Ruggiero, N.J.

Revision History  

• Version 1.0: 2008-11-11
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2018-01-31
  Changes: Experimental preparation
• Version 1.3: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description