3FGW

One chain form of the 66.3 kDa protein

• PDB DOI: https://doi.org/10.2210/pdb3FGW/pdb

• Classification: HYDROLASE
• Organism(s): Mus musculus
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2008-12-08 Released: 2009-09-15 
• Deposition Author(s): Lakomek, K., Dickmanns, A., Ficner, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.249 
• R-Value Work: 0.223 
• R-Value Observed: 0.224 

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

• PubMed: 19706171 
• DOI: https://doi.org/10.1186/1472-6807-9-56
• Primary Citation of Related Structures:  
  3FGR, 3FGT, 3FGW


• 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-terminal fragment.

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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. [e-mail]

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 65.62 kDa 
• Atom Count: 4,487 
• Modelled Residue Count: 529 
• Deposited Residue Count: 559 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative phospholipase B-like 2	A	559	Mus musculus	Mutation(s): 0  Gene Names: AAG44101 EC: 3.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q3TCN2 (Mus musculus) Explore Q3TCN2  Go to UniProtKB:  Q3TCN2
IMPC:  MGI:1919022

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	C [auth A], D [auth A], E [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
IOD	I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M
GOL	F [auth A], G [auth A], H [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
NA	P [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.249 
• R-Value Work: 0.223 
• R-Value Observed: 0.224 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 146.69	α = 90
b = 88.11	β = 111.1
c = 73.55	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-09-15 
Deposition Author(s): Lakomek, K., Dickmanns, A., Ficner, R.

Revision History  

• Version 1.0: 2009-09-15
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
• Version 2.1: 2023-11-01
  Changes: Data collection, Database references, Refinement description, Structure summary