1VCX

Neutron Crystal Structure of the Wild Type Rubredoxin from Pyrococcus Furiosus at 1.5A Resolution


Experimental Data Snapshot

  • Method: NEUTRON DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.186 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history

Literature

Neutron crystallographic study on rubredoxin from Pyrococcus furiosus by BIX-3, a single-crystal diffractometer for biomacromolecules

Kurihara, K.Tanaka, I.Chatake, T.Adams, M.W.W.Jenney Jr., F.E.Moiseeva, N.Bau, R.Niimura, N.

(2004) Proc.Natl.Acad.Sci.USA 101: 11215-11220

  • DOI: 10.1073/pnas.0403807101

  • PubMed Abstract: 
  • The structure of a partially deuterated rubredoxin from the hyperthermophilic archaeon Pyrococcus furiosus, an organism that grows optimally at 100 degrees C, was determined by using the neutron single-crystal diffractometer dedicated for biological ...

    The structure of a partially deuterated rubredoxin from the hyperthermophilic archaeon Pyrococcus furiosus, an organism that grows optimally at 100 degrees C, was determined by using the neutron single-crystal diffractometer dedicated for biological macromolecules (BIX-3) at the JRR-3M reactor of the Japan Atomic Energy Research Institute. Data were collected at room temperature up to a resolution of 1.5 A, and the completeness factor of the data set was 81.9%. The model contains 306 H and 50 D atoms. A total of 37 hydration water molecules were identified, with 15 having all three atoms fully located and the remaining D2O molecules partially defined. The model has been refined to final agreement factors of R = 18.6% and Rfree = 21.7%. Several orientations of the O-D bonds of side chains, whose assignments from x-ray data were previously ambiguous, were clearly visible in the neutron structure. Although most backbone N-H bonds had undergone some degree of H/D exchange throughout the rubredoxin molecule, 5 H atom positions still had distinctly negative (H) peaks. The neutron Fourier maps clearly showed the details of an extensive set of H bonds involving the ND3+ terminus that may contribute to the unusual thermostability of this molecule.


    Organizational Affiliation

    Neutron Science Research Center, Japan Atomic Energy Research Institute, Tokai, Ibaraki 319-1195, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Rubredoxin
A
53Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)Mutation(s): 0 
Gene Names: rub
Find proteins for P24297 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Go to UniProtKB:  P24297
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FE
Query on FE

Download SDF File 
Download CCD File 
A
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
DOD
Query on DOD

Download SDF File 
Download CCD File 
A
DEUTERATED WATER
D2 O
XLYOFNOQVPJJNP-ZSJDYOACSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: NEUTRON DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.186 
Software Package:
Software NamePurpose
SCALEPACKdata scaling
X-PLORphasing
CNSrefinement
CNSphasing
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-08-10
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.3: 2018-03-07
    Type: Data collection
  • Version 1.4: 2018-07-11
    Type: Data collection
  • Version 1.5: 2018-07-18
    Type: Data collection