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- PDB-1a7r: FV FRAGMENT OF MOUSE MONOCLONAL ANTIBODY D1.3 (BALB/C, IGG1, K) V... -

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Basic information

Entry
Database: PDB / ID: 1a7r
TitleFV FRAGMENT OF MOUSE MONOCLONAL ANTIBODY D1.3 (BALB/C, IGG1, K) VARIANT CHAIN L GLU81->ASP
Components
  • IGG1-KAPPA D1.3 FV (HEAVY CHAIN)
  • IGG1-KAPPA D1.3 FV (LIGHT CHAIN)
KeywordsIMMUNOGLOBULIN
Function / homology
Function and homology information


immunoglobulin complex / immunoglobulin mediated immune response / antigen binding / adaptive immune response / extracellular region
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
Immunoglobulin kappa chain variable 12-41 / Ig heavy chain V region PJ14
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsMarks, C. / Henrick, K. / Winter, G.
Citation
Journal: To be Published
Title: X-Ray Structures of D1.3 Fv Mutants
Authors: Marks, C. / Henrick, K. / Winter, G.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1994
Title: Bound Water Molecules and Conformational Stabilization Help Mediate an Antigen-Antibody Association
Authors: Bhat, T.N. / Bentley, G.A. / Boulot, G. / Greene, M.I. / Tello, D. / Dall'Acqua, W. / Souchon, H. / Schwarz, F.P. / Mariuzza, R.A. / Poljak, R.J.
#2: Journal: Nature / Year: 1990
Title: Small Rearrangements in Structures of Fv and Fab Fragments of Antibody D1.3 On Antigen Binding
Authors: Bhat, T.N. / Bentley, G.A. / Fischmann, T.O. / Boulot, G. / Poljak, R.J.
History
DepositionMar 16, 1998Processing site: BNL
Revision 1.0Apr 29, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name / _struct_ref_seq_dif.details
Revision 1.4Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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: IGG1-KAPPA D1.3 FV (LIGHT CHAIN)
H: IGG1-KAPPA D1.3 FV (HEAVY CHAIN)


Theoretical massNumber of molelcules
Total (without water)24,5442
Polymers24,5442
Non-polymers00
Water2,000111
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1680 Å2
ΔGint-9 kcal/mol
Surface area9920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.245, 90.245, 56.235
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Antibody IGG1-KAPPA D1.3 FV (LIGHT CHAIN)


Mass: 11686.950 Da / Num. of mol.: 1 / Fragment: FV FRAGMENT / Mutation: E81D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Variant: CHAIN L, E81D / Production host: Escherichia coli (E. coli) / References: UniProt: P01635
#2: Antibody IGG1-KAPPA D1.3 FV (HEAVY CHAIN)


Mass: 12857.275 Da / Num. of mol.: 1 / Fragment: FV FRAGMENT
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Variant: CHAIN L, E81D / Production host: Escherichia coli (E. coli) / References: UniProt: P01820
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE ANTIBODY IS SECRETED INTO PERIPLASMIC SPACE. VH AND VL DOMAINS ARE COVALENTLY LINKED AND THEY ...THE ANTIBODY IS SECRETED INTO PERIPLASMIC SPACE. VH AND VL DOMAINS ARE COVALENTLY LINKED AND THEY ASSOCIATE SPONTANEOUSLY. CHAIN IDENTIFIER *L* STANDS FOR LIGHT-CHAIN RESIDUES, *H* FOR HEAVY-CHAIN RESIDUES. THE NUMBERING SYSTEM USED IN THIS ENTRY IS SEQUENTIAL, FROM 1 - 107 FOR THE LIGHT CHAIN AND FROM 201 - 316 FOR THE HEAVY CHAIN.
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.33 Å3/Da / Density % sol: 47.25 %

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Data collection

DiffractionMean temperature: 269 K
Diffraction sourceWavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 1, 1992
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→13.89 Å / Num. obs: 96880 / % possible obs: 94.7 % / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 15.94 Å2 / Rmerge(I) obs: 0.08
Reflection shellResolution: 2→2.05 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.297 / % possible all: 43.3

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
AGROVATA/ROTAVATAdata reduction
ALMN/CCP4model building
CCP4refinement
Agrovatadata scaling
ROTAVATAdata scaling
CCP4(ALMN)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1VFA

1vfa


Resolution: 2.01→6 Å / σ(F): 0 /
RfactorNum. reflection
Rwork0.17 -
all-14719
obs-14719
Displacement parametersBiso mean: 18.25 Å2
Refinement stepCycle: LAST / Resolution: 2.01→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1721 0 0 111 1832
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0190.02
X-RAY DIFFRACTIONp_angle_d0.050.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0510.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.3051.5
X-RAY DIFFRACTIONp_mcangle_it1.962
X-RAY DIFFRACTIONp_scbond_it2.522
X-RAY DIFFRACTIONp_scangle_it3.5843
X-RAY DIFFRACTIONp_plane_restr0.0160.02
X-RAY DIFFRACTIONp_chiral_restr0.1450.12
X-RAY DIFFRACTIONp_singtor_nbd0.1640.2
X-RAY DIFFRACTIONp_multtor_nbd0.1760.2
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1380.2
X-RAY DIFFRACTIONp_planar_tor2.613
X-RAY DIFFRACTIONp_staggered_tor19.120
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor13.815
X-RAY DIFFRACTIONp_special_tor15

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