4PZL

The crystal structure of adenylate kinase from Francisella tularensis subsp. tularensis SCHU S4

• PDB DOI: https://doi.org/10.2210/pdb4PZL/pdb

• Classification: TRANSFERASE
• Organism(s): Francisella tularensis subsp. tularensis SCHU S4
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-03-31 Released: 2014-04-16 
• Deposition Author(s): Tan, K., Zhou, M., Kwon, K., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.237 
• R-Value Work: 0.191 
• R-Value Observed: 0.194 

Literature

The crystal structure of adenylate kinase from Francisella tularensis subsp. tularensis SCHU S4

Tan, K., Zhou, M., Kwon, K., Anderson, W.F., 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 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: 109.68 kDa 
• Atom Count: 7,129 
• Modelled Residue Count: 892 
• Deposited Residue Count: 968 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenylate kinase	A, B, C, D	242	Francisella tularensis subsp. tularensis SCHU S4	Mutation(s): 0  Gene Names: adk, FTT_1161 EC: 2.7.4.3
UniProt
Find proteins for Q5NFR4 (Francisella tularensis subsp. tularensis (strain SCHU S4 / Schu 4)) Explore Q5NFR4  Go to UniProtKB:  Q5NFR4

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	K [auth C]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL	G [auth A], J [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
FMT	F [auth A], H [auth B], L [auth D], M [auth D]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N
CA	E [auth A], I [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-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: 0.237 
• R-Value Work: 0.191 
• R-Value Observed: 0.194 
• Space Group: P 3₂
• Diffraction Data: https://doi.org/10.18430/m34pzl

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.022	α = 90
b = 65.022	β = 90
c = 214.732	γ = 120

Software Package:

Software Name	Purpose
SBC-Collect	data collection
SHELXD	phasing
MLPHARE	phasing
DM	model building
ARP	model building
WARP	model building
HKL-3000	phasing
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-04-16 
Deposition Author(s): Tan, K., Zhou, M., Kwon, K., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2014-04-16
  Type: Initial release
  
• Version 1.1: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary