4PZL | pdb_00004pzl

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 (Depositor), 0.236 (DCC) 
• R-Value Work: 
  0.191 (Depositor), 0.193 (DCC) 
• R-Value Observed: 
  0.194 (Depositor) 

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 
• Modeled 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 (Depositor), 0.236 (DCC) 
• R-Value Work:  0.191 (Depositor), 0.193 (DCC) 
• R-Value Observed: 0.194 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m34pzl

Space Group: P 3₂

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