4JHS

Crystal structure of a C-terminal two domain fragment of human beta-2-glycoprotein 1

• PDB DOI: https://doi.org/10.2210/pdb4JHS/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Trichoplusia ni
• Mutation(s): No 


• Deposited: 2013-03-05 Released: 2013-04-24 
• Deposition Author(s): Bonanno, J.B., Toro, R., Gizzi, A., Chan, M.K., Garrett-Thomson, S.C., Patel, H., Lim, S., Matikainen, B., Celikgil, A., Garforth, S., Hillerich, B., Seidel, R., Rand, J.H., Almo, S.C., New York Structural Genomics Research Consortium (NYSGRC), Atoms-to-Animals: The Immune Function Network (IFN)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.250 
• R-Value Work: 0.207 

Starting Model: experimental

Literature

Crystal structure of a C-terminal two domain fragment of human beta-2-glycoprotein 1

Bonanno, J.B., Toro, R., Gizzi, A., Chan, M.K., Garrett-Thomson, S.C., Patel, H., Lim, S., Matikainen, B., Celikgil, A., Garforth, S., Hillerich, B., Seidel, R., Rand, J.H., Almo, S.C.

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: 21.01 kDa 
• Atom Count: 1,112 
• Modelled Residue Count: 142 
• Deposited Residue Count: 180 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-glycoprotein 1	A	180	Homo sapiens	Mutation(s): 0  Gene Names: APOH, B2G1
UniProt & NIH Common Fund Data Resources
Find proteins for P02749 (Homo sapiens) Explore P02749  Go to UniProtKB:  P02749
PHAROS:  P02749 GTEx:  ENSG00000091583

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A], C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.250 
• R-Value Work: 0.207 
• Space Group: I 4₁ 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 157.79	α = 90
b = 157.79	β = 90
c = 157.79	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
MOSFLM	data reduction
MOLREP	phasing
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-04-24 
Deposition Author(s): Bonanno, J.B., Toro, R., Gizzi, A., Chan, M.K., Garrett-Thomson, S.C., Patel, H., Lim, S., Matikainen, B., Celikgil, A., Garforth, S., Hillerich, B., Seidel, R., Rand, J.H., Almo, S.C., New York Structural Genomics Research Consortium (NYSGRC), Atoms-to-Animals: The Immune Function Network (IFN)

Revision History  

• Version 1.0: 2013-04-24
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Refinement description
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description