4M9O | pdb_00004m9o

Crystal Structure of monomeric zebrafish beta-2-microglobulin

• PDB DOI: https://doi.org/10.2210/pdb4M9O/pdb

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


• Deposited: 2013-08-15 Released: 2014-09-24 
• Deposition Author(s): Wu, P.H., Lai, M.H., Li, C.H., Chang, C.C., Chen, C.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.14 Å
• R-Value Free: 
  0.231 (Depositor), 0.218 (DCC) 
• R-Value Work: 
  0.172 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.175 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of monomeric zebrafish beta-2-microglobulin

Wu, P.H., Lai, M.H., Li, C.H., Chang, C.C., Chen, C.J.

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: 12.44 kDa 
• Atom Count: 837 
• Modeled Residue Count: 97 
• Deposited Residue Count: 107 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	A	107	Danio rerio	Mutation(s): 0  Gene Names: b2m, beta-2-microglobulin
UniProt
Find proteins for Q04475 (Danio rerio) Explore Q04475  Go to UniProtKB:  Q04475

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.14 Å
• R-Value Free:  0.231 (Depositor), 0.218 (DCC) 
• R-Value Work:  0.172 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.175 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.084	α = 90
b = 50.926	β = 90
c = 54.07	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
AMoRE	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-09-24 
Deposition Author(s): Wu, P.H., Lai, M.H., Li, C.H., Chang, C.C., Chen, C.J.

Revision History  

• Version 1.0: 2014-09-24
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-10-30
  Changes: Structure summary