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- PDB-1dvf: IDIOTOPIC ANTIBODY D1.3 FV FRAGMENT-ANTIIDIOTOPIC ANTIBODY E5.2 F... -

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Basic information

Entry
Database: PDB / ID: 1dvf
TitleIDIOTOPIC ANTIBODY D1.3 FV FRAGMENT-ANTIIDIOTOPIC ANTIBODY E5.2 FV FRAGMENT COMPLEX
Components
  • (FV D1.3) x 2
  • (FV E5.2) x 2
KeywordsCOMPLEX (IDIOTOPE-ANTIIDIOTOPE) / IMMUNOGLOBULIN
Function / homology
Function and homology information


immunoglobulin complex / immunoglobulin mediated immune response / antigen binding / adaptive immune response / immune response / extracellular region / metal ion binding
Similarity search - Function
: / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily ...: / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
VDJ complex / Immunoglobulin kappa chain variable 12-41 / Ig kappa chain V-V region HP 123E6 / Ig heavy chain V region PJ14
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsBraden, B.C. / Fields, B.A. / Ysern, X. / Dall'Acqua, W. / Goldbaum, F.A. / Poljak, R.J. / Mariuzza, R.A.
Citation
Journal: J.Mol.Biol. / Year: 1996
Title: Crystal structure of an Fv-Fv idiotope-anti-idiotope complex at 1.9 A resolution.
Authors: Braden, B.C. / Fields, B.A. / Ysern, X. / Dall'Acqua, W. / Goldbaum, F.A. / Poljak, R.J. / Mariuzza, R.A.
#1: Journal: Nature / Year: 1995
Title: Molecular Basis of Antigen Mimicry by an Anti-Idiotope
Authors: Fields, B.A. / Goldbaum, F.A. / Ysern, X. / Poljak, R.J. / Mariuzza, R.A.
#2: Journal: J.Mol.Biol. / Year: 1994
Title: Crystallization and Preliminary X-Ray Diffraction Study of an Idiotope-Anti-Idiotope Fv-Fv Complex
Authors: Goldbaum, F.A. / Fields, B.A. / Cauerhff, A. / Ysern, X. / Houdusse, A. / Eisele, J.L. / Poljak, R.J. / Mariuzza, R.A.
History
DepositionApr 13, 1996Processing site: BNL
Revision 1.0Aug 17, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Jun 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 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 16, 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
A: FV D1.3
B: FV D1.3
C: FV E5.2
D: FV E5.2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,0037
Polymers49,8074
Non-polymers1963
Water2,828157
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5670 Å2
ΔGint-85 kcal/mol
Surface area18220 Å2
MethodPISA
2
A: FV D1.3
B: FV D1.3
C: FV E5.2
D: FV E5.2
hetero molecules

A: FV D1.3
B: FV D1.3
C: FV E5.2
D: FV E5.2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,00714
Polymers99,6148
Non-polymers3926
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area11860 Å2
ΔGint-227 kcal/mol
Surface area36010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.800, 79.400, 51.500
Angle α, β, γ (deg.)90.00, 100.20, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-1159-

ZN

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Components

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Antibody , 4 types, 4 molecules ABCD

#1: Antibody FV D1.3


Mass: 11858.171 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: IGG1, KAPPA / Source: (gene. exp.) Mus musculus (house mouse) / Strain: BALB-C / Production host: Escherichia coli (E. coli) / References: UniProt: P01635
#2: Antibody FV D1.3


Mass: 12857.275 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: IGG1, KAPPA / Source: (gene. exp.) Mus musculus (house mouse) / Strain: BALB/C / Production host: Escherichia coli (E. coli) / References: UniProt: P01820
#3: Antibody FV E5.2


Mass: 11770.961 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: IGG1, KAPPA / Source: (gene. exp.) Mus musculus (house mouse) / Strain: BALB-C / Production host: Escherichia coli (E. coli) / References: UniProt: P01646
#4: Antibody FV E5.2


Mass: 13320.795 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: IGG1, KAPPA / Source: (gene. exp.) Mus musculus (house mouse) / Strain: BALB/C / Production host: Escherichia coli (E. coli) / References: UniProt: A0NA69*PLUS

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Non-polymers , 2 types, 160 molecules

#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.09 Å3/Da / Density % sol: 60.21 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: Goldbaum, F.A., (1994) J.Mol.Biol., 241, 739.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
215 %(w/v)PEG80001reservoir
30.2 Mammonium sulfate1reservoir
40.1 MHEPES1reservoir

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 41404 / % possible obs: 82.5 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.085
Reflection
*PLUS
Highest resolution: 1.9 Å / Num. measured all: 105969

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Processing

Software
NameClassification
XENGENdata collection
X-PLORmodel building
X-PLORrefinement
XENGENdata reduction
X-PLORphasing
RefinementResolution: 1.9→7 Å / σ(F): 2
RfactorNum. reflection
Rfree0.249 -
Rwork0.194 -
obs0.194 32539
Refinement stepCycle: LAST / Resolution: 1.9→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3494 0 3 157 3654
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_deg2
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 Rfree: 0.235
Solvent computation
*PLUS
Displacement parameters
*PLUS

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