3O4P

DFPase at 0.85 Angstrom resolution (H atoms included)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.85 Å
  • R-Value Free: 0.121 
  • R-Value Work: 0.103 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Hydrogen atoms in protein structures: high-resolution X-ray diffraction structure of the DFPase.

Elias, M.Liebschner, D.Koepke, J.Lecomte, C.Guillot, B.Jelsch, C.Chabriere, E.

(2013) BMC Res Notes 6: 308-308

  • DOI: https://doi.org/10.1186/1756-0500-6-308
  • Primary Citation of Related Structures:  
    3O4P

  • PubMed Abstract: 

    Hydrogen atoms represent about half of the total number of atoms in proteins and are often involved in substrate recognition and catalysis. Unfortunately, X-ray protein crystallography at usual resolution fails to access directly their positioning, mainly because light atoms display weak contributions to diffraction. However, sub-Ångstrom diffraction data, careful modeling and a proper refinement strategy can allow the positioning of a significant part of hydrogen atoms. A comprehensive study on the X-ray structure of the diisopropyl-fluorophosphatase (DFPase) was performed, and the hydrogen atoms were modeled, including those of solvent molecules. This model was compared to the available neutron structure of DFPase, and differences in the protein and the active site solvation were noticed. A further examination of the DFPase X-ray structure provides substantial evidence about the presence of an activated water molecule that may constitute an interesting piece of information as regard to the enzymatic hydrolysis mechanism.


  • Organizational Affiliation

    Weizmann Institute of Science, Biological Chemistry, Rehovot, Israel.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Diisopropyl-fluorophosphatase314Loligo vulgarisMutation(s): 0 
EC: 3.1.8.2 (PDB Primary Data), 3.8.2.2 (UniProt)
UniProt
Find proteins for Q7SIG4 (Loligo vulgaris)
Explore Q7SIG4 
Go to UniProtKB:  Q7SIG4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7SIG4
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 9 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MES
Query on MES

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A]
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
PGE
Query on PGE

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N [auth A],
O [auth A]
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
ME2
Query on ME2

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V [auth A]1-ETHOXY-2-(2-METHOXYETHOXY)ETHANE
C7 H16 O3
CNJRPYFBORAQAU-UHFFFAOYSA-N
PEG
Query on PEG

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T [auth A],
U [auth A]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL
Query on GOL

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B [auth A],
C [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
DXE
Query on DXE

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P [auth A],
Q [auth A]
1,2-DIMETHOXYETHANE
C4 H10 O2
XTHFKEDIFFGKHM-UHFFFAOYSA-N
MXE
Query on MXE

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R [auth A],
S [auth A]
2-METHOXYETHANOL
C3 H8 O2
XNWFRZJHXBZDAG-UHFFFAOYSA-N
EDO
Query on EDO

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F [auth A]
G [auth A]
H [auth A]
I [auth A]
J [auth A]
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA
Query on CA

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W [auth A],
X [auth A]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.85 Å
  • R-Value Free: 0.121 
  • R-Value Work: 0.103 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.114α = 90
b = 81.849β = 90
c = 86.467γ = 90
Software Package:
Software NamePurpose
MoProrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-08-17
    Type: Initial release
  • Version 1.1: 2013-08-14
    Changes: Database references
  • Version 1.2: 2024-02-21
    Changes: Data collection, Database references, Derived calculations
  • Version 1.3: 2024-04-03
    Changes: Refinement description