3SO5 | pdb_00003so5

Crystal structure of an Immunoglobulin I-set domain of Lrig3 protein (Lrig3) from MUS MUSCULUS at 1.70 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3SO5/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-06-29 Released: 2011-07-27 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG), Partnership for Stem Cell Biology (STEMCELL)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.216 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.206 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.206 (Depositor) 

Literature

Crystal structure of an Immunoglobulin I-set domain of Lrig3 protein (Lrig3) from MUS MUSCULUS at 1.70 A resolution

Joint Center for Structural Genomics (JCSG), Partnership for Stem Cell Biology (STEMCELL)

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 25.78 kDa 
• Atom Count: 1,938 
• Modeled Residue Count: 217 
• Deposited Residue Count: 224 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Leucine-rich repeats and immunoglobulin-like domains protein 3	A, B	112	Mus musculus	Mutation(s): 0  Gene Names: BC065142, Kiaa3016, Lrig3
UniProt & NIH Common Fund Data Resources
Find proteins for Q6P1C6 (Mus musculus) Explore Q6P1C6  Go to UniProtKB:  Q6P1C6
IMPC:  MGI:2443955

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], G [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CL	D [auth A], E [auth A], F [auth A], H [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MLY	A, B	L-PEPTIDE LINKING	C8 H18 N2 O2		LYS
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.216 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.206 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.206 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33SO5

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.634	α = 90
b = 63.634	β = 90
c = 113.405	γ = 90

Software Package:

Software Name	Purpose
MolProbity	model building
PDB_EXTRACT	data extraction
SHELX	phasing
SHARP	phasing
SCALA	data scaling
BUSTER-TNT	refinement
MOSFLM	data reduction
SHELXD	phasing
BUSTER	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-07-27 
Deposition Author(s): Joint Center for Structural Genomics (JCSG), Partnership for Stem Cell Biology (STEMCELL)

Revision History  

• Version 1.0: 2011-07-27
  Type: Initial release
  
• Version 1.1: 2015-10-21
  Changes: Structure summary
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2023-02-01
  Changes: Database references, Derived calculations