2HEK | pdb_00002hek

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.220 (Depositor), 0.237 (DCC) 
  • R-Value Work: 
    0.175 (Depositor), 0.197 (DCC) 
  • R-Value Observed: 
    0.177 (Depositor) 

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Ligand Structure Quality Assessment 


This is version 1.4 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 Struct Biol Cryst Commun 63: 369-374

  • DOI: https://doi.org/10.1107/S1744309107018945
  • Primary Citation Related Structures: 
    2HEK

  • 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-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.

Macromolecule Content 

  • Total Structure Weight: 90.76 kDa 
  • Atom Count: 6,705 
  • Modeled Residue Count: 738 
  • Deposited Residue Count: 742 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Hypothetical protein
A, B
371Aquifex aeolicusMutation(s): 0 
UniProt
Find proteins for O67745 (Aquifex aeolicus (strain VF5))
Explore O67745 
Go to UniProtKB:  O67745
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO67745
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GDP

Query on GDP



Download:Ideal Coordinates CCD File
G [auth A],
H [auth A]
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
PO4

Query on PO4



Download:Ideal Coordinates CCD File
C [auth A],
O [auth B],
P [auth B],
Q [auth B]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL

Query on GOL



Download:Ideal Coordinates CCD File
I [auth A]
J [auth A]
K [auth A]
L [auth A]
M [auth A]
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
W [auth B],
X [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
BR

Query on BR



Download:Ideal Coordinates CCD File
S [auth B]BROMIDE ION
Br
CPELXLSAUQHCOX-UHFFFAOYSA-M
ZN

Query on ZN



Download:Ideal Coordinates CCD File
D [auth A],
R [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
E [auth A],
F [auth A],
T [auth B],
U [auth B],
V [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.220 (Depositor), 0.237 (DCC) 
  • R-Value Work:  0.175 (Depositor), 0.197 (DCC) 
  • R-Value Observed: 0.177 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.687α = 90
b = 144.413β = 90
c = 144.677γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-07-04
    Type: Initial release
  • Version 1.1: 2008-02-06
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description
  • Version 1.4: 2024-02-14
    Changes: Data collection, Database references, Derived calculations