1WC7

FAB FRAGMENT OF PLP-DEPENDENT CATALYTIC ANTIBODY 15A9 IN COMPLEX WITH PHOSPHOPYRIDOXYL-L-ALANINE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.33 Å
  • R-Value Free: 0.309 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Structure of a Pseudomerohedrally Twinned Monoclinic Crystal Form of a Pyridoxal Phosphate-Dependent Catalytic Antibody

Golinelli-Pimpaneau, B.

(2005) Acta Crystallogr.,Sect.D 61: 472

  • DOI: 10.1107/S0907444905003331

  • PubMed Abstract: 
  • The purification, crystallization and structure determination at 2.3 A resolution of the complex of the pyridoxal-5'-phosphate (PLP) dependent catalytic antibody 15A9 with a phosphopyridoxyl-L-alanine (PPL-L-alanine) substrate analogue are described. ...

    The purification, crystallization and structure determination at 2.3 A resolution of the complex of the pyridoxal-5'-phosphate (PLP) dependent catalytic antibody 15A9 with a phosphopyridoxyl-L-alanine (PPL-L-alanine) substrate analogue are described. The crystal belongs to space group P2(1), with two molecules in the asymmetric unit related by non-crystallographic symmetry. The unit-cell parameters are a = 63.5, b = 81.7, c = 79.3 A and beta is fortuitously 90 degrees . Refinement of the structure converged at unacceptably high R factors. Although the traditional analysis of intensity distribution did not indicate twinning, pseudomerohedral twinning was revealed by a newer test based on local intensity differences [Padilla & Yeates (2003), Acta Cryst. D59, 1124-1130]. When the potential twinning operator was included in SHELX, the structure could be satisfactorily refined with a twinning fraction of 0.46, indicating a nearly perfect hemihedrally twinned crystal. One of the active sites is occupied by the phosphopyridoxyl-L-alanine ligand, while one iodide ion mimics the cofactor phosphate group in the other. Four other iodide ions are present in the structure: two are involved in specific intermolecular contacts and two dictate the conformation of the CDRH3 loop in each molecule.


    Related Citations: 
    • Monoclonal Antibodies Against N-Alpha-(5'-Phosphopyridoxyl)-L-Lysine.
      Gramatikova, S.I.,Christen, P.
      (1997) J.Biol.Chem. 272: 9779


    Organizational Affiliation

    Laboratoire d'Enzymologie et de Biochimie Structurales, B√Ętiment 34, CNRS, 1 Avenue de la Terrasse, 91190 Gif-sur-Yvette, France. beatrice.golinelli@lebs.cnrs-gif.fr




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
FAB FRAGMENT OF CATALYTIC ANTIBODY 15A9, LIGHT CHAIN
A, L
213N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
FAB FRAGMENT OF CATALYTIC ANTIBODY 15A9, HEAVY CHAIN
B, H
226N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PP3
Query on PP3

Download SDF File 
Download CCD File 
A
ALANYL-PYRIDOXAL-5'-PHOSPHATE
PYRIDOXYL-ALANINE-5-PHOSPHATE; VITAMIN B6 COMPLEXED WITH ALANINE
C11 H17 N2 O7 P
WACJCHFWJNNBPR-ZETCQYMHSA-N
 Ligand Interaction
IOD
Query on IOD

Download SDF File 
Download CCD File 
A, B, H, L
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.33 Å
  • R-Value Free: 0.309 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 63.476α = 90.00
b = 81.691β = 89.98
c = 79.330γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-11-30
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2019-01-30
    Type: Data collection, Experimental preparation, Other
  • Version 1.4: 2019-05-22
    Type: Data collection, Refinement description