1NGX

Chimeric Germline Fab 7g12 with jeffamine fragment bound

• PDB DOI: https://doi.org/10.2210/pdb1NGX/pdb

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


• Deposited: 2002-12-18 Released: 2003-03-18 
• Deposition Author(s): Yin, J., Andryski, S.E., Beuscher, A.B., Stevens, R.C., Schultz, P.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.250 
• R-Value Work: 0.225 

Literature

Structural evidence for substrate strain in antibody catalysis

Yin, J., Andryski, S.E., Beuscher, A.B., Stevens, R.C., Schultz, P.G.

(2003) Proc Natl Acad Sci U S A 100: 856-861

• PubMed: 12552112 
• DOI: https://doi.org/10.1073/pnas.0235873100
• Primary Citation of Related Structures:  
  1N7M, 1NGW, 1NGX, 1NGY, 1NGZ


• PubMed Abstract: 
  

  The crystal structure of the Michaelis complex between the Fab fragment of ferrochelatase antibody 7G12 and its substrate mesoporphyrin has been solved to 2.6-A resolution. The antibody-bound mesoporphyrin clearly adopts a nonplanar conformation and reveals that the antibody catalyzes the porphyrin metallation reaction by straining/distorting the bound substrate toward the transition-state configuration. The crystal structures of the Fab fragment of the germ-line precursor antibody to 7G12 and its complex with the hapten N-methylmesoporphyrin have also been solved. A comparison of these structures with the corresponding structures of the affinity-matured antibody 7G12 reveals the molecular mechanism by which the immune system evolves binding energy to catalyze this reaction.

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Organizational Affiliation: 

Department of Chemistry, University of California, Berkeley, CA 94720, USA.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

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

Macromolecule Content

• Total Structure Weight: 94.08 kDa 
• Atom Count: 7,256 
• Modelled Residue Count: 858 
• Deposited Residue Count: 858 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Germline Metal Chelatase Catalytic Antibody, Light chain	A, C [auth L]	213	Mus musculus, Homo sapiens This entity is chimeric	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Germline Metal Chelatase Catalytic Antibody, Heavy chain	B, D [auth H]	216	Mus musculus, Homo sapiens This entity is chimeric	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
JEF	E [auth B], F [auth H]	O-(O-(2-AMINOPROPYL)-O'-(2-METHOXYETHYL)POLYPROPYLENE GLYCOL 500) C30 H63 N O10 ICCXIDTYQFYPNV-RUMGZKRTSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.250 
• R-Value Work: 0.225 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.666	α = 90
b = 64.723	β = 92.58
c = 93.382	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
EPMR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-03-18 
Deposition Author(s): Yin, J., Andryski, S.E., Beuscher, A.B., Stevens, R.C., Schultz, P.G.

Revision History  

• Version 1.0: 2003-03-18
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2018-01-31
  Changes: Experimental preparation
• Version 1.4: 2024-11-13
  Changes: Data collection, Database references, Derived calculations, Structure summary