1BAF

2.9 ANGSTROMS RESOLUTION STRUCTURE OF AN ANTI-DINITROPHENYL-SPIN-LABEL MONOCLONAL ANTIBODY FAB FRAGMENT WITH BOUND HAPTEN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Work: 0.195 

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This is version 1.3 of the entry. See complete history

Literature

2.9 A resolution structure of an anti-dinitrophenyl-spin-label monoclonal antibody Fab fragment with bound hapten.

Brunger, A.T.Leahy, D.J.Hynes, T.R.Fox, R.O.

(1991) J.Mol.Biol. 221: 239-256


  • PubMed Abstract: 
  • The crystal structure of the Fab fragment of the murine monoclonal anti-dinitrophenyl-spin-label antibody AN02 complexed with its hapten has been solved at 2.9 A resolution using a novel molecular replacement method. Prior to translation searches, a ...

    The crystal structure of the Fab fragment of the murine monoclonal anti-dinitrophenyl-spin-label antibody AN02 complexed with its hapten has been solved at 2.9 A resolution using a novel molecular replacement method. Prior to translation searches, a large number of the most likely rotation function solutions were subjected to a rigid body refinement against the linear correlation coefficient between intensities of observed and calculated structure factors. First, the overall orientation of the search model and then the orientations and positions of the four Fab domains (VH, VL, CH1 and CL) were refined. This procedure clearly identified the correct orientation of the search model. The refined search model was then subjected to translation searches which unambiguously determined the enantiomer and position in the unit cell of the crystal. The successful search model was refined 2.5 A crystal structure of the Fab fragment of HyHel-5 from which non-matching residues in the variable domains had been removed. HyHel-5 is a murine monoclonal antibody whose heavy and light chains are of the same subclass (gamma 1, kappa, respectively) as AN02. After molecular replacement the structure of the AN02 Fab has been refined using simulated annealing in combination with model building and conjugate gradient refinement to a current crystallographic R-factor of 19.5% for 12,129 unique reflections between 8.0 and 2.9 A. The root-mean-square (r.m.s.) deviation from ideal bond lengths is 0.014 A, and the r.m.s. deviation from ideal bond angles is 3.1 degrees. The electron density reveals the hapten sitting in a pocket formed by the loops of the complementarity determining region. The dinitrophenyl ring of the hapten is sandwiched between the indole rings of Trp96 of the heavy-chain and Trp91 of the light-chain. The positioning of the hapten and general features of the combining site are in good agreement with the results of earlier nuclear magnetic resonance experiments.


    Related Citations: 
    • Sequences of 12 Monoclonal Anti-Dinitrophenyl Spin-Label Antibodies for NMR Studies
      Leahy, D.J.,Rule, G.S.,Whittaker, M.M.,Mcconnell, H.M.
      (1988) Proc.Natl.Acad.Sci.USA 85: 3661
    • Monoclonal Antibodies to a Nitroxide Lipid Hapten
      Balakrishnan, K.,Hsu, F.J.,Hafeman, D.G.,Mcconnell, H.M.
      (1982) Biochim.Biophys.Acta 721: 30
    • Crystallization of an Anti-2,2,6, 6-Tetramethyl-1-Piperidinyloxy-Dinitrophenyl Monoclonal Antibody Fab Fragment with and without Bound Hapten
      Leahy, D.J.,Hynes, T.R.,Mcconnell, H.M.,Fox, R.O.
      (1988) J.Mol.Biol. 203: 829


    Organizational Affiliation

    Howard Hughes Medical Institute, Yale University, New Haven, CT 06511.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
IGG1-KAPPA AN02 FAB (LIGHT CHAIN)
L
214N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
IGG1-KAPPA AN02 FAB (HEAVY CHAIN)
H
217N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NPP
Query on NPP

Download SDF File 
Download CCD File 
L
N-(2-AMINO-ETHYL)-4,6-DINITRO-N'-(2,2,6,6-TETRAMETHYL-1-OXY-PIPERIDIN-4-YL)-BENZENE-1,3-DIAMINE
C17 H27 N6 O5
FOFORQYTEPGQOY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Work: 0.195 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 73.230α = 90.00
b = 73.230β = 90.00
c = 373.800γ = 120.00
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORphasing
X-PLORrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1994-01-31
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2013-09-18
    Type: Source and taxonomy