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- PDB-1hil: STRUCTURAL EVIDENCE FOR INDUCED FIT AS A MECHANISM FOR ANTIGEN-AN... -

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Basic information

Entry
Database: PDB / ID: 1hil
TitleSTRUCTURAL EVIDENCE FOR INDUCED FIT AS A MECHANISM FOR ANTIGEN-ANTIBODY RECOGNITION
Components
  • IGG2A-KAPPA 17/9 FAB (HEAVY CHAIN)
  • IGG2A-KAPPA 17/9 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 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: IGG2A-KAPPA 17/9 FAB (LIGHT CHAIN)
B: IGG2A-KAPPA 17/9 FAB (HEAVY CHAIN)
C: IGG2A-KAPPA 17/9 FAB (LIGHT CHAIN)
D: IGG2A-KAPPA 17/9 FAB (HEAVY CHAIN)


Theoretical massNumber of molelcules
Total (without water)95,1784
Polymers95,1784
Non-polymers00
Water2,882160
1
A: IGG2A-KAPPA 17/9 FAB (LIGHT CHAIN)
B: IGG2A-KAPPA 17/9 FAB (HEAVY CHAIN)


Theoretical massNumber of molelcules
Total (without water)47,5892
Polymers47,5892
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3360 Å2
ΔGint-19 kcal/mol
Surface area19530 Å2
MethodPISA
2
C: IGG2A-KAPPA 17/9 FAB (LIGHT CHAIN)
D: IGG2A-KAPPA 17/9 FAB (HEAVY CHAIN)


Theoretical massNumber of molelcules
Total (without water)47,5892
Polymers47,5892
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3550 Å2
ΔGint-19 kcal/mol
Surface area19290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.040, 82.800, 73.400
Angle α, β, γ (deg.)90.00, 122.60, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: RESIDUES PRO 8, PRO 95, AND PRO 141 OF LIGHT CHAINS AND RESIDUES PRO 149, PRO 151 AND PRO 200 OF HEAVY CHAINS ARE CIS PROLINES.

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Components

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


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


Mass: 23677.441 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: GenBank: 533229
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE TWO MOLECULES ARE IN SEQUENTIAL ORDER IN THE COORDINATE FILE. THE FAB-FRAGMENT IS NUMBERED ...THE TWO MOLECULES ARE IN SEQUENTIAL ORDER IN THE COORDINATE FILE. THE FAB-FRAGMENT IS NUMBERED ACCORDING TO KABAT (E.A.KABAT, T.T.WU, H.M.PERRY, K.S.GOTTESMAN, AND C.FOELLER, SEQUENCES OF PROTEINS OF IMMUNOLOGICAL INTEREST, 1991).

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49.19 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / PH range low: 6.5 / PH range high: 5.6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlFab1drop
20.2 Mimidazole malate1drop
30.1 M1dropNaCl
430-39 %PEG6001drop
50.2 Mimidazole malate1reservoir
60.1 M1reservoirNaCl
730-39 %PEG6001reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2 Å / Rmerge(I) obs: 0.09

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2→6 Å / Rfactor Rwork: 0.195 / Rfactor obs: 0.195 / σ(F): 2
Refinement stepCycle: LAST / Resolution: 2→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6605 0 0 160 6765
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
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
Highest resolution: 2 Å / Lowest resolution: 6 Å / σ(F): 2 / Rfactor obs: 0.195
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 3

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