5HRJ | pdb_00005hrj

Crystal structure of the scavenger receptor cysteine-rich domain 5 (SRCR5) from porcine CD163

PDB DOI: https://doi.org/10.2210/pdb5HRJ/pdb

Classification: ENDOCYTOSIS
Organism(s): Sus scrofa
Expression System: Komagataella pastoris
Mutation(s): No

Deposited: 2016-01-23 Released: 2017-07-19
Deposition Author(s): Ma, H., Jiang, L., Qiao, S., Zhang, G., Li, R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.253 (Depositor), 0.273 (DCC)
R-Value Work:
0.213 (Depositor)
R-Value Observed:
0.215 (Depositor)

Starting Model: experimental
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This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of the scavenger receptor cysteine-rich domain 5 (SRCR5) from porcine CD163

Ma, H., Jiang, L., Qiao, S., Zhang, G., Li, R.

To be published.

Macromolecule Content

Total Structure Weight: 11.64 kDa
Atom Count: 809
Modeled Residue Count: 101
Deposited Residue Count: 109
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Scavenger receptor cysteine-rich type 1 protein M130	A	109	Sus scrofa	Mutation(s): 0 Gene Names: CD163, M130
UniProt
Find proteins for Q2VL90 (Sus scrofa) Explore Q2VL90 Go to UniProtKB: Q2VL90
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q2VL90
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.253 (Depositor), 0.273 (DCC)
R-Value Work: 0.213 (Depositor)
R-Value Observed: 0.215 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 29.72	α = 90
b = 73.01	β = 90
c = 87.4	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data collection
XDS	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2017-07-19

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2017-07-19
Type: Initial release
Version 1.1: 2017-10-04
Changes: Data collection
Version 1.2: 2023-11-08
Changes: Data collection, Database references, Refinement description
Version 1.3: 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.