4JZK | pdb_00004jzk

Crystal Structure of Adenylate kinase of E. Coli with ADP/AMP bound

• PDB DOI: https://doi.org/10.2210/pdb4JZK/pdb

• Classification: TRANSFERASE
• Organism(s): Escherichia coli O104:H4 str. 2009EL-2071
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-04-03 Released: 2014-04-30 
• Deposition Author(s): Cho, Y.-J., Agafonov, R., Kern, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.63 Å
• R-Value Free: 
  0.252 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.214 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.216 (Depositor) 

Literature

Crystal structure of E. Coli Adenylate kinase with ADP and AMP bound

Cho, Y.-J., Agafonov, R., Kern, D.

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)

Macromolecule Content 

• Total Structure Weight: 48.79 kDa 
• Atom Count: 4,109 
• Modeled Residue Count: 428 
• Deposited Residue Count: 428 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenylate kinase	A, B	214	Escherichia coli O104:H4 str. 2009EL-2071	Mutation(s): 0  Gene Names: adk, O3O_06175 EC: 2.7.4.3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	C [auth A], E [auth B]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
AMP	D [auth A], F [auth B]	ADENOSINE MONOPHOSPHATE C10 H14 N5 O7 P UDMBCSSLTHHNCD-KQYNXXCUSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.63 Å
• R-Value Free:  0.252 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.214 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.216 (Depositor) 

Space Group: P 2₁ 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.96	α = 90
b = 78.8	β = 90
c = 83.03	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-04-30 
Deposition Author(s): Cho, Y.-J., Agafonov, R., Kern, D.

Revision History  

• Version 1.0: 2014-04-30
  Type: Initial release
  
• Version 1.1: 2024-02-28
  Changes: Data collection, Database references, Derived calculations