5I0Z | pdb_00005i0z

Crystal structure of the single domain catalytic antibody 3D8-VH

• PDB DOI: https://doi.org/10.2210/pdb5I0Z/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-02-04 Released: 2016-02-24 
• Deposition Author(s): Park, S.Y., Kim, J.S.
• Funding Organization(s): Chonnam National University

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.262 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.218 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.220 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the single domain catalytic antibody 3D8-VH

Park, S.Y., Kim, B.N.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 31.63 kDa 
• Atom Count: 2,230 
• Modeled Residue Count: 240 
• Deposited Residue Count: 286 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
catalytic DNA antibody	A, B	143	Mus musculus	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.262 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.218 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.220 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.775	α = 90
b = 85.82	β = 100.87
c = 50.202	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
iMOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-02-24 
Deposition Author(s): Park, S.Y., Kim, J.S.

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Funding Organization	Location	Grant Number
Chonnam National University	Korea, Republic Of	2015-0597

Revision History  

• Version 1.0: 2016-02-24
  Type: Initial release
  
• Version 1.1: 2017-08-30
  Changes: Data collection, Derived calculations
• Version 1.2: 2017-11-15
  Changes: Source and taxonomy
• Version 1.3: 2023-11-08
  Changes: Data collection, Database references, Refinement description
• Version 1.4: 2024-10-30
  Changes: Structure summary