1VDG | pdb_00001vdg

Crystal structure of LIR1.01, one of the alleles of LIR1

• PDB DOI: https://doi.org/10.2210/pdb1VDG/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2004-03-22 Released: 2005-08-02 
• Deposition Author(s): Shiroishi, M., Rasubala, L., Kuroki, K., Amano, K., Tsuchiya, N., Tokunaga, K., Kohda, D., Maenaka, K.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.301 (Depositor), 0.239 (DCC) 
• R-Value Work: 
  0.241 (Depositor), 0.221 (DCC) 
• R-Value Observed: 
  0.250 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of LIR1.03, one of the alleles of LIR1

Shiroishi, M., Rasubala, L., Kuroki, K., Amano, K., Tsuchiya, N., Tokunaga, K., Kohda, D., Maenaka, K.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 44 kDa 
• Atom Count: 3,010 
• Modeled Residue Count: 374 
• Deposited Residue Count: 394 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Leukocyte immunoglobulin-like receptor subfamily B member 1	A, B	197	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NHL6 (Homo sapiens) Explore Q8NHL6  Go to UniProtKB:  Q8NHL6
PHAROS:  Q8NHL6

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.301 (Depositor), 0.239 (DCC) 
• R-Value Work:  0.241 (Depositor), 0.221 (DCC) 
• R-Value Observed: 0.250 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.969	α = 90
b = 93.22	β = 107.82
c = 57.773	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-08-02 
Deposition Author(s): Shiroishi, M., Rasubala, L., Kuroki, K., Amano, K., Tsuchiya, N., Tokunaga, K., Kohda, D., Maenaka, K.

Revision History  

• Version 1.0: 2005-08-02
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-10-25
  Changes: Data collection, Database references, Refinement description
• Version 1.4: 2024-11-06
  Changes: Structure summary