3NN8 | pdb_00003nn8

Crystal structure of engineered antibody fragment based on 3D5

• PDB DOI: https://doi.org/10.2210/pdb3NN8/pdb

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


• Deposited: 2010-06-23 Released: 2011-06-29 
• Deposition Author(s): Lieberman, R.L., Maynard, J.A., Drury, J.E., Pai, J., Culver, J.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 
  0.238 (Depositor), 0.213 (DCC) 
• R-Value Work: 
  0.183 (Depositor), 0.194 (DCC) 
• R-Value Observed: 
  0.186 (Depositor) 

Starting Model: experimental

Literature

Peptide-binding single chain Antibody fragment (SCFV) chaperones for protein co-crystallization

Pai, J., Culver, J.A., Drury, J.E., Lieberman, R.L., Maynard, J.A.

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)

Biological Assembly 2  

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

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

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 108.56 kDa 
• Atom Count: 7,272 
• Modeled Residue Count: 947 
• Deposited Residue Count: 1,024 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Engineered scFv	A, B, C, D	256	Mus musculus	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free:  0.238 (Depositor), 0.213 (DCC) 
• R-Value Work:  0.183 (Depositor), 0.194 (DCC) 
• R-Value Observed: 0.186 (Depositor) 

Space Group: F 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 266.637	α = 90
b = 266.637	β = 90
c = 266.637	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-06-29 
Deposition Author(s): Lieberman, R.L., Maynard, J.A., Drury, J.E., Pai, J., Culver, J.A.

Revision History  

• Version 1.0: 2011-06-29
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-09-06
  Changes: Data collection, Database references, Refinement description
• Version 2.0: 2024-03-27
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Polymer sequence, Refinement description, Source and taxonomy, Structure summary
• Version 2.1: 2024-11-20
  Changes: Structure summary