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- PDB-1a7q: FV FRAGMENT OF MOUSE MONOCLONAL ANTIBODY D1.3 (BALB/C, IGG1, K) H... -

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Basic information

Entry
Database: PDB / ID: 1a7q
TitleFV FRAGMENT OF MOUSE MONOCLONAL ANTIBODY D1.3 (BALB/C, IGG1, K) HIGH AFFINITY EXPRESSED VARIANT CONTAINING SER26L->GLY, ILE29L->THR, GLU81L->ASP, THR97L->SER, PRO240H->LEU, ASP258H->ALA, LYS281H->GLU, ASN283H->ASP AND LEU312H->VAL
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 / immune response / extracellular space
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 / Immunoglobulins / Immunoglobulin-like fold / 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 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 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 21, 2022Group: Database references / Refinement description / Category: database_2 / 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 1.4Aug 9, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.5Oct 23, 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)24,2742
Polymers24,2742
Non-polymers00
Water84747
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1660 Å2
ΔGint-10 kcal/mol
Surface area9770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.307, 90.307, 56.847
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: 11457.653 Da / Num. of mol.: 1 / Fragment: FV FRAGMENT / Mutation: S26G, I29T, E81D, T97S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse)
Variant: CHAIN L, S26G, I29T, E81D, T97S, CHAIN H, P240L, D258A, K281E, N283D, L312V
Production host: Escherichia coli (E. coli) / References: GenBank: 545862, UniProt: P01635*PLUS
#2: Antibody IGG1-KAPPA D1.3 FV (HEAVY CHAIN)


Mass: 12816.200 Da / Num. of mol.: 1 / Fragment: FV FRAGMENT / Mutation: P240L, D258A, K281E, N283D, L312V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse)
Variant: CHAIN L, S26G, I29T, E81D, T97S, CHAIN H, P240L, D258A, K281E, N283D, L312V
Production host: Escherichia coli (E. coli) / References: GenBank: 896294, UniProt: P01820*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 2.39 Å3/Da / Density % sol: 48.46 %

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Data collection

DiffractionMean temperature: 269 K
Diffraction sourceWavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 1, 1992
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→13.68 Å / Num. obs: 134765 / % possible obs: 97.8 % / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Biso Wilson estimate: 25.08 Å2 / Rmerge(I) obs: 0.097
Reflection shellResolution: 2→2.05 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.3 / % possible all: 79.7

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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→6 Å / σ(F): 0 /
RfactorNum. reflection
Rwork0.178 -
all-15836
obs-15836
Displacement parametersBiso mean: 21.7 Å2
Refinement stepCycle: LAST / Resolution: 2→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1681 0 0 47 1728
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0190.02
X-RAY DIFFRACTIONp_angle_d0.0550.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0580.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.5061.5
X-RAY DIFFRACTIONp_mcangle_it2.2372
X-RAY DIFFRACTIONp_scbond_it2.9782
X-RAY DIFFRACTIONp_scangle_it4.393
X-RAY DIFFRACTIONp_plane_restr0.0150.02
X-RAY DIFFRACTIONp_chiral_restr0.1530.12
X-RAY DIFFRACTIONp_singtor_nbd0.1610.2
X-RAY DIFFRACTIONp_multtor_nbd0.1570.2
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1460.2
X-RAY DIFFRACTIONp_planar_tor2.5193
X-RAY DIFFRACTIONp_staggered_tor18.9320
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor12.3415
X-RAY DIFFRACTIONp_special_tor15

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