4X4X | pdb_00004x4x

Retrofitting antibodies with stabilizing mutations. Herceptin scFv mutant.

• PDB DOI: https://doi.org/10.2210/pdb4X4X/pdb

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


• Deposited: 2014-12-04 Released: 2015-12-23 
• Deposition Author(s): Langley, D.B., Roome, B., Christ, D.
• Funding Organization(s): National Health and Medical Research Council (NHMRC, Australia)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 
  0.269 (Depositor), 0.274 (DCC) 
• R-Value Work: 
  0.226 (Depositor), 0.229 (DCC) 
• R-Value Observed: 
  0.228 (Depositor) 

Literature

Retrofitting antibodies with stabilizing mutations

Langley, D.B., Roome, B., Christ, D.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 52.6 kDa 
• Atom Count: 3,149 
• Modeled Residue Count: 434 
• Deposited Residue Count: 494 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Human Variable Heavy Chain of Herceptin	A, C	140	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Human Variable Light Chain of Herceptin	B, D	107	Homo sapiens	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free:  0.269 (Depositor), 0.274 (DCC) 
• R-Value Work:  0.226 (Depositor), 0.229 (DCC) 
• R-Value Observed: 0.228 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.19	α = 90
b = 91.19	β = 90
c = 114.35	γ = 120

Software Package:

Software Name	Purpose
Blu-Ice	data collection
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing
REFMAC	refinement

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2015-12-23 
Deposition Author(s): Langley, D.B., Roome, B., Christ, D.

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Funding Organization	Location	Grant Number
National Health and Medical Research Council (NHMRC, Australia)	Australia	--

Revision History  

• Version 1.0: 2015-12-23
  Type: Initial release
  
• Version 1.1: 2017-09-06
  Changes: Author supporting evidence, Data collection, Derived calculations
• Version 1.2: 2020-01-08
  Changes: Author supporting evidence
• Version 1.3: 2024-10-30
  Changes: Data collection, Database references, Structure summary