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 

wwPDB Validation 3D Report Full Report


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

  • 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-cry ...

    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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ADENYLATE KINASE
A, B, C, D, E, F
194Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770)Mutation(s): 0 
Gene Names: adkA (adk)
EC: 2.7.4.3
Find proteins for P35028 (Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770))
Go to UniProtKB:  P35028
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download SDF File 
Download CCD File 
F
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
AMP
Query on AMP

Download SDF File 
Download CCD File 
C, D, 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 = 73.510α = 90.00
b = 145.690β = 90.00
c = 172.280γ = 90.00
Software Package:
Software NamePurpose
GETAXphasing
MLPHAREphasing
GETAXmodel building
CCP4data scaling
REFMACrefinement
DMmodel building
MOSFLMdata reduction
DMphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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