4TYP

Crystal structure of an adenylate kinase mutant--AKm1

• PDB DOI: https://doi.org/10.2210/pdb4TYP/pdb

• Classification: TRANSFERASE
• Organism(s): Bacillus subtilis subsp. subtilis str. 168
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2014-07-09 Released: 2014-11-26 
• Deposition Author(s): Moon, S., Bae, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.329 
• R-Value Work: 0.288 
• R-Value Observed: 0.290 

Starting Model: experimental

Literature

Crystal structures of thermally stable adenylate kinase mutants designed by local structural entropy optimization and structure-guided mutagenesis

Moon, S., Bae, E.

(2014) J Korean Soc Appl Biological Chem 57: 661-665

• DOI: https://doi.org/10.1007/s13765-014-4228-4

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)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 101.62 kDa 
• Atom Count: 6,504 
• Modelled Residue Count: 790 
• Deposited Residue Count: 868 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenylate kinase	A [auth C], B, C [auth A], D	217	Bacillus subtilis subsp. subtilis str. 168	Mutation(s): 41  Gene Names: adk, BSU01370 EC: 2.7.4.3
UniProt
Find proteins for P16304 (Bacillus subtilis (strain 168)) Explore P16304  Go to UniProtKB:  P16304

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AP5	E [auth C], G [auth B], I [auth A], J [auth D]	BIS(ADENOSINE)-5'-PENTAPHOSPHATE C20 H29 N10 O22 P5 OIMACDRJUANHTJ-XPWFQUROSA-N
ZN	F [auth B], H [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.329 
• R-Value Work: 0.288 
• R-Value Observed: 0.290 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.641	α = 90
b = 123.338	β = 98.28
c = 86.693	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-11-26 
Deposition Author(s): Moon, S., Bae, E.

Revision History  

• Version 1.0: 2014-11-26
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description, Source and taxonomy