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- PDB-1ifh: A DETAILED ANALYSIS OF THE FREE AND BOUND CONFORMATION OF AN ANTI... -

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Basic information

Entry
Database: PDB / ID: 1ifh
TitleA DETAILED ANALYSIS OF THE FREE AND BOUND CONFORMATION OF AN ANTIBODY: X-RAY STRUCTURES OF ANTI-PEPTIDE FAB 17(SLASH)9 AND THREE DIFFERENT FAB-PEPTIDE COMPLEXES
Components
  • IGG2A-KAPPA 17/9 FAB (HEAVY CHAIN)
  • IGG2A-KAPPA 17/9 FAB (LIGHT CHAIN)
  • INFLUENZA HEMAGGLUTININ HA1 (STRAIN X47) (RESIDUES 101-107)
KeywordsIMMUNOGLOBULIN
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / : / :
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / Resolution: 2.8 Å
AuthorsSchulze-Gahmen, U. / Wilson, I.A.
Citation
Journal: J.Mol.Biol. / Year: 1993
Title: Detailed analysis of the free and bound conformations of an antibody. X-ray structures of Fab 17/9 and three different Fab-peptide complexes.
Authors: Schulze-Gahmen, U. / Rini, J.M. / Wilson, I.A.
#1: 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.
#2: 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
DepositionMay 6, 1993Processing site: BNL
Revision 1.0Oct 31, 1993Provider: 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_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_sheet.number_strands
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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 101-107)


Theoretical massNumber of molelcules
Total (without water)48,4953
Polymers48,4953
Non-polymers00
Water181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4610 Å2
ΔGint-23 kcal/mol
Surface area19670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.100, 103.900, 67.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: CIS PROLINE - PRO L 8 / 2: CIS PROLINE - PRO L 95 / 3: CIS PROLINE - PRO L 141
4: ARG L 211 - ASN L 212 OMEGA ANGLE = 0.020 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
5: CIS PROLINE - PRO H 149 / 6: CIS PROLINE - PRO H 151 / 7: CIS PROLINE - PRO H 200

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Components

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


Mass: 24025.471 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Strain: A/J / 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) / Strain: A/J / References: GenBank: 533229
#3: Protein/peptide INFLUENZA HEMAGGLUTININ HA1 (STRAIN X47) (RESIDUES 101-107)


Mass: 791.804 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.: 1 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsTHERE IS ONE BOUND WATER MOLECULE IN THE BINDING SITE OF THE FAB FRAGMENT.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.62 Å3/Da / Density % sol: 53.09 %
Crystal grow
*PLUS
pH: 6.3 / Method: vapor diffusion, sitting drop / Details: micro seeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
21.6 Msodium phosphate1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 9999 Å / Num. obs: 11779 / Num. measured all: 57732 / Rmerge(I) obs: 0.116

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Processing

Software
NameVersionClassification
X-PLOR3model building
X-PLOR3refinement
X-PLOR3phasing
RefinementResolution: 2.8→10 Å / σ(F): 2 /
RfactorNum. reflection
Rwork0.17 -
obs0.17 57732
Refinement stepCycle: LAST / Resolution: 2.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3390 0 0 1 3391
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
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_deg3.6
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: 10 Å / Num. reflection obs: 57732 / σ(F): 2 / Rfactor obs: 0.17
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 3.6

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