1K6Q | pdb_00001k6q

Crystal structure of antibody Fab fragment D3

• PDB DOI: https://doi.org/10.2210/pdb1K6Q/pdb

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


• Deposited: 2001-10-17 Released: 2002-04-17 
• Deposition Author(s): Faelber, K., Kelley, R.F., Kirchhofer, D., Muller, Y.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.298 (Depositor), 0.300 (DCC) 
• R-Value Work: 
  0.225 (Depositor), 0.225 (DCC) 

Starting Model: other

Literature

The crystal structure of murine Fab D3 at 2.4 A resolution in comparison with the humanised Fab D3h44 (1.85A) provides structural insight into the humanisation process of the D3 anti-tissue factor antibody

Faelber, K., Kelley, R.F., Kirchhofer, D., Muller, Y.A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content 

• Total Structure Weight: 46.45 kDa 
• Atom Count: 3,375 
• Modeled Residue Count: 417 
• Deposited Residue Count: 426 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
immunoglobulin Fab D3, light chain	A [auth L]	210	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
immunoglobulin Fab D3, heavy chain	B [auth H]	216	Mus musculus	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.298 (Depositor), 0.300 (DCC) 
• R-Value Work:  0.225 (Depositor), 0.225 (DCC) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.17	α = 90
b = 77.48	β = 114.75
c = 75.19	γ = 90

Software Package:

Software Name	Purpose
MAR345	data collection
XDS	data reduction
AMoRE	phasing
CNS	refinement
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-04-17 
Deposition Author(s): Faelber, K., Kelley, R.F., Kirchhofer, D., Muller, Y.A.

Revision History  

• Version 1.0: 2002-04-17
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-04-03
  Changes: Data collection, Database references, Refinement description
• Version 1.4: 2024-10-23
  Changes: Structure summary