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.

Experimental Data Snapshot

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

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 5XEP

This is version 1.2 of the entry. See complete history.

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.

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

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chitinase-3-like protein 1	A, B, C, D, E 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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q61362
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A], H [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain G [auth A] Focus chain H [auth A]

Experimental Data & Validation

Experimental Data

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

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Entry History

Deposition Data

Released Date: 2018-04-11

Deposition Author(s):

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.