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- PDB-1igf: CRYSTAL STRUCTURES OF AN ANTIBODY TO A PEPTIDE AND ITS COMPLEX WI... -

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Basic information

Entry
Database: PDB / ID: 1igf
TitleCRYSTAL STRUCTURES OF AN ANTIBODY TO A PEPTIDE AND ITS COMPLEX WITH PEPTIDE ANTIGEN AT 2.8 ANGSTROMS
Components
  • IGG1-KAPPA B13I2 FAB (HEAVY CHAIN)
  • IGG1-KAPPA B13I2 FAB (LIGHT CHAIN)
KeywordsIMMUNOGLOBULIN
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / : / :
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / Resolution: 2.8 Å
AuthorsStanfield, R.L. / Wilson, I.A.
Citation
Journal: Science / Year: 1990
Title: Crystal structures of an antibody to a peptide and its complex with peptide antigen at 2.8 A.
Authors: Stanfield, R.L. / Fieser, T.M. / Lerner, R.A. / Wilson, I.A.
#1: Journal: J.Biol.Chem. / Year: 1989
Title: Preliminary Crystallographic Data and Primary Sequence for Anti-Peptide Fab' B13I2 and its Complex with the C-Helix Peptide from Myohemerythrin
Authors: Stura, E.A. / Stanfield, R.L. / Fieser, T.M. / Balderas, R.S. / Smith, L.R. / Lerner, R.A. / Wilson, I.A.
History
DepositionMar 21, 1991Processing site: BNL
Revision 1.0Apr 15, 1992Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.process_site / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: IGG1-KAPPA B13I2 FAB (LIGHT CHAIN)
H: IGG1-KAPPA B13I2 FAB (HEAVY CHAIN)
M: IGG1-KAPPA B13I2 FAB (LIGHT CHAIN)
J: IGG1-KAPPA B13I2 FAB (HEAVY CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,1345
Polymers95,9134
Non-polymers2211
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.000, 151.700, 80.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: RESIDUES 8, 95, AND 141 OF THE *L* AND *M* CHAINS AND RESIDUES 149 AND 151 OF THE *H* AND *J* CHAINS ARE CIS PROLINES.
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.246, 0.12614, -0.96103), (-0.04309, 0.99194, 0.11916), (0.96831, 0.01209, 0.24946)
Vector: 5.2072, 16.41404, 4.87641)
DetailsTHE TWO FAB' HEAVY CHAINS (RESIDUES 1-227) OF THE ASYMMETRIC UNIT HAVE BEEN ASSIGNED CHAIN INDICATORS *H* AND *J*. THERE ARE TWO FAB MOLECULES PER ASYMMETRIC UNIT. THE NON-CRYSTALLOGRAPHIC TRANSFORMATION PRESENTED ON THE *MTRIX* RECORDS BELOW YIELDS APPROXIMATE COORDINATES FOR MOLECULE 2 WHEN APPLIED TO MOLECULE 1 (COORDINATES OF CHAIN *M* FROM CHAIN *L* AND COORDINATES OF CHAIN *J* FROM CHAIN *H*).

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Components

#1: Antibody IGG1-KAPPA B13I2 FAB (LIGHT CHAIN)


Mass: 24148.803 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Strain: A/J / References: PIR: PC4203
#2: Antibody IGG1-KAPPA B13I2 FAB (HEAVY CHAIN)


Mass: 23807.738 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Strain: A/J / References: PIR: S38864
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
Nonpolymer detailsNAG N 901 IS LINKED TO ASN L 26 OF THE FIRST FAB' FRAGMENT IN THE ASYMMETRIC UNIT. BECAUSE DENSITY ...NAG N 901 IS LINKED TO ASN L 26 OF THE FIRST FAB' FRAGMENT IN THE ASYMMETRIC UNIT. BECAUSE DENSITY FOR THE CORRESPONDING NAG ON THE SECOND FAB' FRAGMENT IS WEAK, THES NAG COORDINATES ARE NOT INCLUDED.
Sequence detailsTHE FAB' FRAGMENT IS NUMBERED BY THE CONVENTION OF E.KABAT (E.A.KABAT,T.T.WU,M.REID-MILLER,H.M. ...THE FAB' FRAGMENT IS NUMBERED BY THE CONVENTION OF E.KABAT (E.A.KABAT,T.T.WU,M.REID-MILLER,H.M.PERRY,K.S.GOTTESMAN, SEQUENCES OF PROTEINS OF IMMUNOLOGICAL INTEREST, 4TH ED., (1987), NATIONAL INSTITUTE OF HEALTH,BETHESDA,MD.).

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.13 Å3/Da / Density % sol: 60.69 %
Crystal grow
*PLUS
pH: 6 / Method: vapor diffusion, sitting drop
Details: taken from Stura, E.A. et al(1989). J. Biol. Chem., 264, 15721-15725.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
116 mg/mlprotein1drop
21 %MPD1reservoir
31.1 Msodium citrate1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

SoftwareName: X-PLOR / Classification: refinement
RefinementResolution: 2.8→8 Å / Rfactor Rwork: 0.18
Refinement stepCycle: LAST / Resolution: 2.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6686 0 14 0 6700
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg3.71
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 8 Å / Rfactor obs: 0.18
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 3.71

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