4IKE | pdb_00004ike

Crystal Structure of a partly open ATP-lid of liganded Adenylate kinase

• PDB DOI: https://doi.org/10.2210/pdb4IKE/pdb

• Classification: TRANSFERASE
• Organism(s): Aquifex aeolicus VF5
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-12-26 Released: 2014-07-02 
• Deposition Author(s): Cho, Y.-J., Kern, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.48 Å
• R-Value Free: 
  0.198 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.161 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.163 (Depositor) 

Literature

The ATP-Lid Opened Adenylate Kinase with Fully Occupied Substrates

Cho, Y.-J., 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: 48.09 kDa 
• Atom Count: 4,060 
• Modeled Residue Count: 412 
• Deposited Residue Count: 412 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenylate kinase	A, B	206	Aquifex aeolicus VF5	Mutation(s): 0  Gene Names: adk, Aquifex, aq_078 EC: 2.7.4.3
UniProt
Find proteins for O66490 (Aquifex aeolicus (strain VF5)) Explore O66490  Go to UniProtKB:  O66490

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.48 Å
• R-Value Free:  0.198 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.161 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.163 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.37	α = 90
b = 61.57	β = 94.33
c = 58.89	γ = 90

Software Package:

Software Name	Purpose
iMOSFLM	data reduction
AutoBuild	model building
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
AutoBuild	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-07-02 
Deposition Author(s): Cho, Y.-J., Kern, D.

Revision History  

• Version 1.0: 2014-07-02
  Type: Initial release
  
• Version 1.1: 2024-02-28
  Changes: Data collection, Database references, Derived calculations