6KR0 | pdb_00006kr0

Crystal structure of HL homo-diabody

• PDB DOI: https://doi.org/10.2210/pdb6KR0/pdb

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


• Deposited: 2019-08-20 Released: 2020-08-26 
• Deposition Author(s): Tanaka, Y.
• Funding Organization(s): Japan Society for the Promotion of Science

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.226 (Depositor), 0.232 (DCC) 
• R-Value Work: 
  0.202 (Depositor), 0.211 (DCC) 
• R-Value Observed: 
  0.203 (Depositor) 

Literature

Association behavior and control of the quality of cancer therapeutic bispecific diabodies expressed in Escherichia coli

Nakazawa, H., Onodera-Sugano, T., Sugiyama, A., Tanaka, Y., Hattori, T., Niide, T., Ogata, H., Asano, R., Kumagai, I., Umetsu, M.

(2020) Biochem Eng J 160

• DOI: https://doi.org/10.1016/j.bej.2020.107636

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 124.53 kDa 
• Atom Count: 7,173 
• Modeled Residue Count: 906 
• Deposited Residue Count: 1,160 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HL diabody	A, B, C, D	290	Homo sapiens	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.226 (Depositor), 0.232 (DCC) 
• R-Value Work:  0.202 (Depositor), 0.211 (DCC) 
• R-Value Observed: 0.203 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.08	α = 90
b = 88.48	β = 90
c = 135.44	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-08-26 
Deposition Author(s): Tanaka, Y.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science	Japan	--

Revision History  

• Version 1.0: 2020-08-26
  Type: Initial release
  
• Version 1.1: 2021-09-08
  Changes: Database references
• Version 1.2: 2024-11-06
  Changes: Data collection, Database references, Structure summary