1S3G | pdb_00001s3g

Crystal structure of adenylate kinase from Bacillus globisporus

• PDB DOI: https://doi.org/10.2210/pdb1S3G/pdb

• Classification: TRANSFERASE
• Organism(s): Sporosarcina globispora
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2004-01-13 Released: 2004-05-04 
• Deposition Author(s): Bae, E., Phillips Jr., G.N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 
  0.288 (Depositor), 0.293 (DCC) 
• R-Value Work: 
  0.223 (Depositor), 0.238 (DCC) 
• R-Value Observed: 
  0.223 (Depositor) 

Starting Model: experimental

Literature

Structures and analysis of highly homologous psychrophilic, mesophilic, and thermophilic adenylate kinases.

Bae, E., Phillips Jr., G.N.

(2004) J Biological Chem 279: 28202-28208

• PubMed: 15100224 
• DOI: https://doi.org/10.1074/jbc.M401865200
• Primary Citation Related Structures: 
  1P3J, 1S3G


• PubMed Abstract: 
  

  The crystal structures of adenylate kinases from the psychrophile Bacillus globisporus and the mesophile Bacillus subtilis have been solved and compared with that from the thermophile Bacillus stearothermophilus. This is the first example we know of where a trio of protein structures has been solved that have the same number of amino acids and a high level of identity (66-74%) and yet come from organisms with different operating temperatures. The enzymes were characterized for their own thermal denaturation and inactivation, and they exhibited the same temperature preferences as their source organisms. The structures of the three highly homologous, dynamic proteins with different temperature-activity profiles provide an opportunity to explore a molecular mechanism of cold and heat adaptation. Their analysis suggests that the maintenance of the balance between stability and flexibility is crucial for proteins to function at their environmental temperatures, and it is achieved by the modification of intramolecular interactions in the process of temperature adaptation.

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Organizational Affiliation: 
• Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 24.9 kDa 
• Atom Count: 1,851 
• Modeled Residue Count: 217 
• Deposited Residue Count: 217 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenylate kinase	A	217	Sporosarcina globispora	Mutation(s): 0  EC: 2.7.4.3
UniProt
Find proteins for P84139 (Sporosarcina globispora) Explore P84139  Go to UniProtKB:  P84139

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free:  0.288 (Depositor), 0.293 (DCC) 
• R-Value Work:  0.223 (Depositor), 0.238 (DCC) 
• R-Value Observed: 0.223 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.288	α = 90
b = 65.288	β = 90
c = 94.378	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling
SOMORE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-05-04 
Deposition Author(s): Bae, E., Phillips Jr., G.N.

Revision History  

• Version 1.0: 2004-05-04
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-08-23
  Changes: Data collection, Database references, Derived calculations, Refinement description