5XEP | pdb_00005xep

Crystal structure of BRP39, a chitinase-like protein, at 2.6 Angstorm resolution

• PDB DOI: https://doi.org/10.2210/pdb5XEP/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2017-04-05 Released: 2018-04-11 
• Deposition Author(s): Mohanty, A.K., Fisher, A.J., Choudhary, S., Kaushik, J.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.231 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.192 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of BRP39, a signalling glycoprotein expressed during mammary gland apoptosis.

Mohanty, A.K., Fisher, A.J., Yu, Z., Pradeep, M.A., Janjanam, J., Kaushik, J.K.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 2 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 258.47 kDa 
• Atom Count: 17,726 
• Modeled Residue Count: 2,158 
• Deposited Residue Count: 2,286 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chitinase-3-like protein 1	A, B, C, D, E, F	381	Mus musculus	Mutation(s): 2  Gene Names: Chi3l1, Brp39, Chil1
UniProt
Find proteins for Q61362 (Mus musculus) Explore Q61362  Go to UniProtKB:  Q61362

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	G [auth A], H [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.231 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.192 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 130.61	α = 90
b = 81.32	β = 105.86
c = 229.33	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-04-11 
Deposition Author(s): Mohanty, A.K., Fisher, A.J., Choudhary, S., Kaushik, J.K.

Revision History  

• Version 1.0: 2018-04-11
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
• Version 1.2: 2024-11-20
  Changes: Structure summary