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- PDB-1dlf: HIGH RESOLUTION CRYSTAL STRUCTURE OF THE FV FRAGMENT FROM AN ANTI... -

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Entry
Database: PDB / ID: 1dlf
TitleHIGH RESOLUTION CRYSTAL STRUCTURE OF THE FV FRAGMENT FROM AN ANTI-DANSYL SWITCH VARIANT ANTIBODY IGG2A(S) CRYSTALLIZED AT PH 5.25
Components(ANTI-DANSYL IMMUNOGLOBULIN IGG2A(S)) x 2
KeywordsIMMUNOGLOBULIN / FV FRAGMENT
Function / homology
Function and homology information


immunoglobulin complex / antigen binding / adaptive immune response / immune response
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-like fold ...: / 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
: / Ig kappa chain V-II region 26-10 / :
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MULTIPLE MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsNakasako, M. / Takahashi, H. / Shimada, I. / Arata, Y.
Citation
Journal: J.Mol.Biol. / Year: 1999
Title: The pH-dependent structural variation of complementarity-determining region H3 in the crystal structures of the Fv fragment from an anti-dansyl monoclonal antibody.
Authors: Nakasako, M. / Takahashi, H. / Shimba, N. / Shimada, I. / Arata, Y.
#1: Journal: J.Mol.Biol. / Year: 1994
Title: Role of the Domain-Domain Interaction in the Construction of the Antigen Combining Site. A Comparative Study by 1H-15N Shift Correlation NMR Spectroscopy of the Fv and Fab Fragments of Anti- ...Title: Role of the Domain-Domain Interaction in the Construction of the Antigen Combining Site. A Comparative Study by 1H-15N Shift Correlation NMR Spectroscopy of the Fv and Fab Fragments of Anti-Dansyl Mouse Monoclonal Antibody
Authors: Takahashi, H. / Tamura, H. / Shimba, N. / Shimada, I. / Arata, Y.
#2: Journal: Biochemistry / Year: 1992
Title: Dynamical Structure of the Antibody Combining Site as Studied by 1H-15N Shift Correlation NMR Spectroscopy
Authors: Takahashi, H. / Suzuki, E. / Shimada, I. / Arata, Y.
#3: Journal: Biochemistry / Year: 1992
Title: Isotope-Edited Nuclear Magnetic Resonance Study of Fv Fragment of Anti-Dansyl Mouse Monoclonal Antibody: Recognition of the Dansyl Hapten
Authors: Odaka, A. / Kim, J.I. / Takahashi, H. / Shimada, I. / Arata, Y.
#4: Journal: Biochemistry / Year: 1991
Title: Preparation of the Fv Fragment from a Short-Chain Mouse Igg2A Anti-Dansyl Monoclonal Antibody and Use of Selectively Deuterated Fv Analogues for Two-Dimensional 1H NMR Analyses of the Antigen-Antibody Interactions
Authors: Takahashi, H. / Igarashi, T. / Shimada, I. / Arata, Y.
#5: Journal: Biochemistry / Year: 1991
Title: Multinuclear NMR Study of the Structure of the Fv Fragment of Anti-Dansyl Mouse Igg2A Antibody
Authors: Takahashi, H. / Odaka, A. / Kawaminami, S. / Matsunaga, C. / Kato, K. / Shimada, I. / Arata, Y.
#6: Journal: J.Am.Chem.Soc. / Year: 1991
Title: Conformation and Stereoselective Reduction of Hapten Side Chain in the Antibody Combining Site
Authors: Kim, T. / Nakano, I. / Higuchi, T. / Hirobe, M. / Shimada, I. / Arata, Y.
#7: Journal: Biochemistry / Year: 1990
Title: Structure of a Mouse Immunoglobulin G that Lacks the Entire Ch1 Domain: Protein Sequencing and Small-Angle X-Ray Scattering Studies
Authors: Igarashi, T. / Sato, M. / Katsube, Y. / Takio, K. / Tanaka, T. / Nakanishi, M. / Arata, Y.
History
DepositionJul 14, 1998Processing site: BNL
Revision 1.0Jul 26, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 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: ANTI-DANSYL IMMUNOGLOBULIN IGG2A(S)
H: ANTI-DANSYL IMMUNOGLOBULIN IGG2A(S)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,9246
Polymers26,5402
Non-polymers3844
Water8,143452
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1970 Å2
ΔGint-56 kcal/mol
Surface area11060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.101, 70.722, 53.464
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody ANTI-DANSYL IMMUNOGLOBULIN IGG2A(S) / ANTI-DANSYL FV FRAGMENT


Mass: 12386.949 Da / Num. of mol.: 1 / Fragment: FV FRAGMENT (VH AND VL DOMAINS) / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell line: HYBRIDOMA / References: UniProt: Q9JL82, UniProt: P01631*PLUS
#2: Antibody ANTI-DANSYL IMMUNOGLOBULIN IGG2A(S) / ANTI-DANSYL FV FRAGMENT


Mass: 14152.787 Da / Num. of mol.: 1 / Fragment: FV FRAGMENT (VH AND VL DOMAINS) / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell line: HYBRIDOMA / References: PIR: PC1213
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 452 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE ANTI-DANSYL FV FRAGMENT RETAINS ITS FULL ANTIGEN BINDING CAPABILITY.
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: 2.01 Å3/Da / Density % sol: 39.8 %
Crystal growpH: 5.25 / Details: pH 5.25
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 293 K / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 mg/mlprotein1drop
20.8 Mammonium sulfate1drop
325 mMsodium cacodylate1drop
41.6 Mammonium sulfate1reservoir
525 mMsodium cacodylate1reservoir

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Data collection

DiffractionMean temperature: 112 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU ULTRAX 18 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 8, 1998
Details: DOUBLE FOCUSSING MIRROR (PT COATED AND NI COATED MIRRORS)
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.45→99 Å / Num. obs: 36158 / % possible obs: 93.9 % / Observed criterion σ(I): 1 / Redundancy: 8.1 % / Rmerge(I) obs: 0.067 / Rsym value: 0.067 / Net I/σ(I): 35.3
Reflection shellResolution: 1.45→1.47 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.265 / Mean I/σ(I) obs: 8.3 / Rsym value: 0.265 / % possible all: 94.4
Reflection
*PLUS
Num. measured all: 280945

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3model building
X-PLOR3refinement
X-PLOR3phasing
RefinementMethod to determine structure: MULTIPLE MOLECULAR REPLACEMENT
Starting model: FV PORTION OF FAB' B13I2 (1IGF)

1igf


Resolution: 1.45→8 Å / Data cutoff high absF: 1000 / Data cutoff low absF: 1 / Isotropic thermal model: GAUSS / σ(F): 2 / Details: ALL ATOMS IN AN ASYMMETRIC UNIT WERE REFINED
RfactorNum. reflection% reflectionSelection details
Rfree0.23 3538 10.2 %RANDOM
Rwork0.183 ---
obs0.183 34689 90.8 %-
Refine analyzeLuzzati coordinate error obs: 0.17 Å
Refinement stepCycle: LAST / Resolution: 1.45→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1837 0 20 452 2309
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
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_deg1.054
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d28.29
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.491
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
LS refinement shellResolution: 1.45→1.46 Å / Total num. of bins used: 40
RfactorNum. reflection% reflection
Rfree0.374 87 12.1 %
Rwork0.364 716 -
obs--87 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.23
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg28.29
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.491

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