3FGT

Two chain form of the 66.3 kDa protein from mouse lacking the linker peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.166 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Initial insight into the function of the lysosomal 66.3 kDa protein from mouse by means of X-ray crystallography

Lakomek, K.Dickmanns, A.Kettwig, M.Urlaub, H.Ficner, R.Luebke, T.

(2009) Bmc Struct.Biol. 9: 56-56

  • DOI: 10.1186/1472-6807-9-56
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The lysosomal 66.3 kDa protein from mouse is a soluble, mannose 6-phosphate containing protein of so far unknown function. It is synthesized as a glycosylated 75 kDa precursor that undergoes limited proteolysis leading to a 28 kDa N- and a 40 kDa C-t ...

    The lysosomal 66.3 kDa protein from mouse is a soluble, mannose 6-phosphate containing protein of so far unknown function. It is synthesized as a glycosylated 75 kDa precursor that undergoes limited proteolysis leading to a 28 kDa N- and a 40 kDa C-terminal fragment.


    Related Citations: 
    • De novo sulfur SAD phasing of the lysosomal 66.3 kDa protein from mouse
      Lakomek, K.,Dickmanns, A.,Mueller, U.,Kollmann, K.,Deuschl, F.,Berndt, A.,Luebke, T.,Ficner, R.
      (2009) Acta Crystallogr.,Sect.D 65: 220


    Organizational Affiliation

    Department of Molecular Structural Biology, Institute of Microbiology and Genetics, GZMB, Georg-August University Goettingen, Justus-von-Liebig-Weg 11, D-37077 Goettingen, Germany. klakome@gwdg.de




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Putative phospholipase B-like 2 28 kDa form
A
202Mus musculusMutation(s): 0 
Gene Names: Plbd2
EC: 3.1.1.-
Find proteins for Q3TCN2 (Mus musculus)
Go to UniProtKB:  Q3TCN2
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Putative phospholipase B-like 2 40 kDa form
B
357Mus musculusMutation(s): 0 
Gene Names: Plbd2
EC: 3.1.1.-
Find proteins for Q3TCN2 (Mus musculus)
Go to UniProtKB:  Q3TCN2
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

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Download CCD File 
A, B
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
7PE
Query on 7PE

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Download CCD File 
B
2-(2-(2-(2-(2-(2-ETHOXYETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHANOL
POLYETHYLENE GLYCOL FRAGMENT
C14 H30 O7
UKXKPKBTMYNOFS-UHFFFAOYSA-N
 Ligand Interaction
PG4
Query on PG4

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Download CCD File 
A, B
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

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Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
OCS
Query on OCS
B
L-PEPTIDE LINKINGC3 H7 N O5 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.166 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 145.570α = 90.00
b = 88.220β = 98.10
c = 63.270γ = 90.00
Software Package:
Software NamePurpose
MAR345data collection
SCALAdata scaling
PDB_EXTRACTdata extraction
REFMACrefinement
MOLREPphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-09-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.2: 2017-11-01
    Type: Refinement description