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 

wwPDB Validation 3D Report Full Report


This is version 1.1 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: 10.1186/1756-0500-6-308

  • 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, m ...

    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-Ã…ngstrom diffraction data, careful modeling and a proper refinement strategy can allow the positioning of a significant part of hydrogen atoms.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Diisopropyl-fluorophosphatase
A
314Loligo vulgarisMutation(s): 0 
EC: 3.1.8.2
Find proteins for Q7SIG4 (Loligo vulgaris)
Go to UniProtKB:  Q7SIG4
Small Molecules
Ligands 9 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DXE
Query on DXE

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A
1,2-DIMETHOXYETHANE
C4 H10 O2
XTHFKEDIFFGKHM-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

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

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A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

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A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
PGE
Query on PGE

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A
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

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A
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
MXE
Query on MXE

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A
2-METHOXYETHANOL
C3 H8 O2
XNWFRZJHXBZDAG-UHFFFAOYSA-N
 Ligand Interaction
ME2
Query on ME2

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A
1-ETHOXY-2-(2-METHOXYETHOXY)ETHANE
C7 H16 O3
CNJRPYFBORAQAU-UHFFFAOYSA-N
 Ligand Interaction
MES
Query on MES

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A
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: 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 = 90.00
b = 81.849β = 90.00
c = 86.467γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
MOSFLMdata reduction
MoProrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-08-17
    Type: Initial release
  • Version 1.1: 2013-08-14
    Type: Database references