7XMP | pdb_00007xmp

High resolution structure of lectin-like Ox-LDL receptor 1 in space group P 32 2 1

PDB DOI: https://doi.org/10.2210/pdb7XMP/pdb

Classification: LIPID BINDING PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli B
Mutation(s): No

Deposited: 2022-04-26 Released: 2023-05-03
Deposition Author(s): Tomar, A., Varughese, K.I., Arockiasamy, A.
Funding Organization(s): Council of Scientific & Industrial Research (CSIR), Department of Science & Technology (DST, India)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.27 Å
R-Value Free:
0.197 (Depositor), 0.202 (DCC)
R-Value Work:
0.158 (Depositor), 0.166 (DCC)
R-Value Observed:
0.160 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

High resolution structure of lectin like Ox-LDL receptor 1 in space group P 32 2 1

Tomar, A., Arockiasamy, A., Varughese, K.I.

To be published.

Macromolecule Content

Total Structure Weight: 15.67 kDa
Atom Count: 1,159
Modeled Residue Count: 128
Deposited Residue Count: 138
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Oxidized low-density lipoprotein receptor 1	A	138	Homo sapiens	Mutation(s): 0 Gene Names: OLR1, CLEC8A, LOX1
UniProt & NIH Common Fund Data Resources
Find proteins for P78380 (Homo sapiens) Explore P78380 Go to UniProtKB: P78380
PHAROS: P78380 GTEx: ENSG00000173391
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P78380
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.27 Å
R-Value Free: 0.197 (Depositor), 0.202 (DCC)
R-Value Work: 0.158 (Depositor), 0.166 (DCC)
R-Value Observed: 0.160 (Depositor)

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.03	α = 90
b = 50.03	β = 90
c = 91.6	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-05-03

Deposition Author(s):

Varughese, K.I.

Arockiasamy, A.

Funding Organization	Location	Grant Number
Council of Scientific & Industrial Research (CSIR)	India	09/512(0221)/2016
Department of Science & Technology (DST, India)	India	EMR/2017/00506

Revision History (Full details and data files)

Version 1.0: 2023-05-03
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Refinement description
Version 1.2: 2024-11-13
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.