2HEK

Crystal structure of O67745, a hypothetical protein from Aquifex aeolicus at 2.0 A resolution.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.997 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.175 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure of O67745_AQUAE, a hypothetical protein from Aquifex aeolicus.

Oganesyan, V.Adams, P.D.Jancarik, J.Kim, R.Kim, S.H.

(2007) Acta Crystallogr.,Sect.F 63: 369-374

  • DOI: 10.1107/S1744309107018945

  • PubMed Abstract: 
  • Using single-wavelength anomalous dispersion data obtained from a gold-derivatized crystal, the X-ray crystal structure of the protein 067745_AQUAE from the prokaryotic organism Aquifex aeolicus has been determined to a resolution of 2.0 A. Amino-aci ...

    Using single-wavelength anomalous dispersion data obtained from a gold-derivatized crystal, the X-ray crystal structure of the protein 067745_AQUAE from the prokaryotic organism Aquifex aeolicus has been determined to a resolution of 2.0 A. Amino-acid residues 1-371 of the 44 kDa protein were identified by Pfam as an HD domain and a member of the metal-dependent phosphohydrolase superfamily (accession No. PF01966). Although three families from this large and diverse group of enzymatic proteins are represented in the PDB, the structure of 067745_AQUAE reveals a unique fold that is unlike the others and that is likely to represent a new subfamily, further organizing the families and characterizing the proteins. Data are presented that provide the first insights into the structural organization of the proteins within this clan and a distal alternative GDP-binding domain outside the metal-binding active site is proposed.


    Organizational Affiliation

    Berkeley Structural Genomics Center, Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Hypothetical protein
A, B
371Aquifex aeolicus (strain VF5)Mutation(s): 0 
Find proteins for O67745 (Aquifex aeolicus (strain VF5))
Go to UniProtKB:  O67745
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

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A
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
PO4
Query on PO4

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A, B
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
ZN
Query on ZN

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A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
BR
Query on BR

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B
BROMIDE ION
Br
CPELXLSAUQHCOX-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.997 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.175 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 107.687α = 90.00
b = 144.413β = 90.00
c = 144.677γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-07-04
    Type: Initial release
  • Version 1.1: 2008-02-06
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.3: 2017-10-18
    Type: Refinement description