2J45

Water structure of T. Aquaticus Ffh NG Domain At 1.1A Resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.14 Å
  • R-Value Free: 0.154 
  • R-Value Work: 0.119 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Analysis of Protein Hydration in Ultra-High Resolution Structures of the Srp Gtpase Ffh

Ramirez, U.D.Freymann, D.M.

(2006) Acta Crystallogr.,Sect.D 62: 1520

  • DOI: 10.1107/S0907444906040807
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Two new structures of the SRP GTPase Ffh have been determined at 1.1 A resolution and provide the basis for comparative examination of the extensive water structure of the apo conformation of these GTPases. A set of well defined water-binding positio ...

    Two new structures of the SRP GTPase Ffh have been determined at 1.1 A resolution and provide the basis for comparative examination of the extensive water structure of the apo conformation of these GTPases. A set of well defined water-binding positions have been identified in the active site of the two-domain ;NG' GTPase, as well as at two functionally important interfaces. The water hydrogen-bonding network accommodates alternate conformations of the protein side chains by undergoing local rearrangements and, in one case, illustrates binding of a solute molecule within the active site by displacement of water molecules without further disruption of the water-interaction network. A subset of the water positions are well defined in several lower resolution structures, including those of different nucleotide-binding states; these appear to function in maintaining the protein structure. Consistent arrangements of surface water between three different ultrahigh-resolution structures provide a framework for beginning to understand how local water structure contributes to protein-ligand and protein-protein binding in the SRP GTPases.


    Related Citations: 
    • Structural Basis for Mobility in the 1.1A Crystal Structure of the Ng Domain of T. Aquaticus Ffh
      Ramirez, U.D.,Minasov, G.,Focia, P.J.,Stroud, R.,Walter, P.,Kuhn, P.,Freymann, D.M.
      (2002) J.Mol.Biol. 320: 783


    Organizational Affiliation

    Department of Molecular Pharmacology and Biological Chemistry, Northwestern University, Chicago, IL 60611, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SIGNAL RECOGNITION PARTICLE PROTEIN
A, B
297Thermus aquaticusMutation(s): 0 
Gene Names: ffh
Find proteins for O07347 (Thermus aquaticus)
Go to UniProtKB:  O07347
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MRD
Query on MRD

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Download CCD File 
A, B
(4R)-2-METHYLPENTANE-2,4-DIOL
C6 H14 O2
SVTBMSDMJJWYQN-RXMQYKEDSA-N
 Ligand Interaction
EDO
Query on EDO

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Download CCD File 
B
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
MES
Query on MES

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Download CCD File 
A, B
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.14 Å
  • R-Value Free: 0.154 
  • R-Value Work: 0.119 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 108.602α = 90.00
b = 54.303β = 99.36
c = 99.776γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-11-30
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2019-05-22
    Type: Data collection, Derived calculations, Other, Refinement description