1NKS

ADENYLATE KINASE FROM SULFOLOBUS ACIDOCALDARIUS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.57 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.164 

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This is version 1.2 of the entry. See complete history


Literature

The structure of a trimeric archaeal adenylate kinase.

Vonrhein, C.Bonisch, H.Schafer, G.Schulz, G.E.

(1998) J Mol Biol 282: 167-179

  • DOI: 10.1006/jmbi.1998.2003
  • Primary Citation of Related Structures:  
    1NKS

  • PubMed Abstract: 
  • The adenylate kinase from the hyperthermophilic archaean species Sulfolobus acidocaldarius has been cloned, expressed in Escherichia coli, purified and crystallized. The crystal structure was elucidated by multiple isomorphous replacement and non-crystallographic density averaging ...

    The adenylate kinase from the hyperthermophilic archaean species Sulfolobus acidocaldarius has been cloned, expressed in Escherichia coli, purified and crystallized. The crystal structure was elucidated by multiple isomorphous replacement and non-crystallographic density averaging. The structure was refined at 2.6 A (1 A=0.1 nm) resolution. The enzyme is trimeric, in contrast to previous solution measurements that suggested a dimeric structure, and in contrast to the vast majority of adenylate kinases, which are monomeric. In large parts of each subunit the chain fold resembles the known enzyme structure from eubacteria and eukaryotes although the sequence homology is negligible. Since the asymmetric unit contains two trimers with and without bound AMP at the AMP sites and with an ADP at one of the six ATP sites, the analysis shows the enzyme in several states. The conformational differences between these states resemble those of other adenylate kinases. Because of sequence homology, the structure presented provides a good model for the methanococcal adenylate kinases.


    Organizational Affiliation

    Institut für Organische Chemie und Biochemie, Albertstr. 21, Freiburg im Breisgau, D-79104, Germany.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ADENYLATE KINASE
A, B, C, D, E, F
A, B, C, D, E, F
194Sulfolobus acidocaldariusMutation(s): 0 
EC: 2.7.4.3
UniProt
Find proteins for P35028 (Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770))
Explore P35028 
Go to UniProtKB:  P35028
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP35028
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download Ideal Coordinates CCD File 
J [auth F]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
AMP
Query on AMP

Download Ideal Coordinates CCD File 
G [auth C],
H [auth D],
I [auth F]
ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.57 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.164 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.51α = 90
b = 145.69β = 90
c = 172.28γ = 90
Software Package:
Software NamePurpose
MLPHAREphasing
GETAXmodel building
DMmodel building
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
GETAXphasing
DMphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1998-12-09
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance