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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.253 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.213 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.215 (Depositor) 

Starting Model: experimental

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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

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

Macromolecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.253 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.213 (Depositor), 0.220 (DCC) 
• 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

Entry History 

Deposition Data

• Released Date: 2017-07-19 
Deposition Author(s): Ma, H., Jiang, L., Qiao, S., Zhang, G., Li, R.

Revision History  

• 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