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- PDB-1hin: STRUCTURAL EVIDENCE FOR INDUCED FIT AS A MECHANISM FOR ANTIBODY-A... -

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Basic information

Entry
Database: PDB / ID: 1hin
TitleSTRUCTURAL EVIDENCE FOR INDUCED FIT AS A MECHANISM FOR ANTIBODY-ANTIGEN RECOGNITION
Components
  • IGG2A-KAPPA 17/9 FAB (HEAVY CHAIN)
  • IGG2A-KAPPA 17/9 FAB (LIGHT CHAIN)
  • INFLUENZA HEMAGGLUTININ HA1 (STRAIN X47) (RESIDUES 100-107)
KeywordsIMMUNOGLOBULIN
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / : / :
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / Resolution: 3.1 Å
AuthorsRini, J.M. / Wilson, I.A.
Citation
Journal: Science / Year: 1992
Title: Structural evidence for induced fit as a mechanism for antibody-antigen recognition.
Authors: Rini, J.M. / Schulze-Gahmen, U. / Wilson, I.A.
#1: Journal: J.Biol.Chem. / Year: 1988
Title: Preliminary Crystallographic Data, Primary Sequence, and Binding Data for an Anti-Peptide Fab and its Complex with a Synthetic Peptide from Influenza Virus Hemagglutinin
Authors: Schulze-Gahmen, U. / Rini, J.M. / Arevalo, J. / Stura, E.A. / Kenten, J.H. / Wilson, I.A.
History
DepositionJul 8, 1992Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ref_seq_dif / struct_sheet
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details / _struct_sheet.number_strands
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: IGG2A-KAPPA 17/9 FAB (LIGHT CHAIN)
H: IGG2A-KAPPA 17/9 FAB (HEAVY CHAIN)
P: INFLUENZA HEMAGGLUTININ HA1 (STRAIN X47) (RESIDUES 100-107)


Theoretical massNumber of molelcules
Total (without water)48,5183
Polymers48,5183
Non-polymers00
Water39622
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.500, 73.400, 62.700
Angle α, β, γ (deg.)90.00, 117.10, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: RESIDUES PRO L 8, PRO L 95, PRO L 141 , PRO H 149, PRO H 151, AND PRO H 200 ARE CIS PROLINES.

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Components

#1: Antibody IGG2A-KAPPA 17/9 FAB (LIGHT CHAIN)


Mass: 23911.369 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / References: PIR: A31790
#2: Antibody IGG2A-KAPPA 17/9 FAB (HEAVY CHAIN)


Mass: 23677.441 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / References: GenBank: 533229
#3: Protein/peptide INFLUENZA HEMAGGLUTININ HA1 (STRAIN X47) (RESIDUES 100-107)


Mass: 928.940 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.68 Å3/Da / Density % sol: 54.1 %
Crystal grow
*PLUS
pH: 5.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mMammonium acetate1reservoir
250 mM1reservoirMnCl2
32-4 %PEG6001reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 3.1 Å / Rmerge(I) obs: 0.1

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 3.1→8 Å / Rfactor Rwork: 0.22 / Rfactor obs: 0.22 / σ(F): 2
Refinement stepCycle: LAST / Resolution: 3.1→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3410 0 0 22 3432
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.019
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_deg3.9
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
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.22 / Rfactor Rwork: 0.22
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 3.9

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