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- PDB-1jfq: ANTIGEN-BINDING FRAGMENT OF THE MURINE ANTI-PHENYLARSONATE ANTIBO... -

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Basic information

Entry
Database: PDB / ID: 1jfq
TitleANTIGEN-BINDING FRAGMENT OF THE MURINE ANTI-PHENYLARSONATE ANTIBODY 36-71, "FAB 36-71"
Components(ANTIGEN-BINDING FRAGMENT OF ANTI-PHENYLARSONATE ANTIBODY) x 2
KeywordsIMMUNE SYSTEM / immunoglobulin
Function / homology
Function and homology information


immunoglobulin production / positive regulation of B cell activation / phagocytosis, recognition / phagocytosis, engulfment / immunoglobulin complex, circulating / immunoglobulin receptor binding / immunoglobulin complex / complement activation, classical pathway / antigen binding / B cell receptor signaling pathway ...immunoglobulin production / positive regulation of B cell activation / phagocytosis, recognition / phagocytosis, engulfment / immunoglobulin complex, circulating / immunoglobulin receptor binding / immunoglobulin complex / complement activation, classical pathway / antigen binding / B cell receptor signaling pathway / adaptive immune response / defense response to bacterium / immune response / external side of plasma membrane / innate 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 / Immunoglobulins / 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Ig kappa chain V-V region HP 91A3 / Ig heavy chain V region 36-65 / :
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsParhami-Seren, B. / Viswanathan, M. / Strong, R.K. / Margolies, M.N.
CitationJournal: J.Immunol. / Year: 2001
Title: Structural analysis of mutants of high-affinity and low-affinity p-azophenylarsonate-specific antibodies generated by alanine scanning of heavy chain complementarity-determining region 2.
Authors: Parhami-Seren, B. / Viswanathan, M. / Strong, R.K. / Margolies, M.N.
History
DepositionJun 21, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Aug 16, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 999SEQUENCE The sequence database reference for the molecules in the this entry is not available

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: ANTIGEN-BINDING FRAGMENT OF ANTI-PHENYLARSONATE ANTIBODY
H: ANTIGEN-BINDING FRAGMENT OF ANTI-PHENYLARSONATE ANTIBODY


Theoretical massNumber of molelcules
Total (without water)47,5732
Polymers47,5732
Non-polymers00
Water2,018112
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3770 Å2
ΔGint-24 kcal/mol
Surface area19350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.130, 73.050, 46.780
Angle α, β, γ (deg.)90.00, 104.48, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody ANTIGEN-BINDING FRAGMENT OF ANTI-PHENYLARSONATE ANTIBODY


Mass: 23715.094 Da / Num. of mol.: 1 / Fragment: LIGHT CHAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): HYBRIDOMA CELLS / Production host: Mus musculus (house mouse) / References: UniProt: Q91WF8, UniProt: P01648*PLUS
#2: Antibody ANTIGEN-BINDING FRAGMENT OF ANTI-PHENYLARSONATE ANTIBODY


Mass: 23857.559 Da / Num. of mol.: 1 / Fragment: HEAVY CHAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse) / References: UniProt: P01747
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 112 / Source method: isolated from a natural source / Formula: H2O

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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: 47.29 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 8000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Method: vapor diffusion
Details: Rose, D.R., (1990) Proc.Natl.Acad.Sci.USA, 87, 338.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
114.9 %(w/w)PEG80001drop
24.0 mg/mlprotein1drop
350 mMphosphate1drop
40.5 %(w/w)1dropNaN3
58.5 %PEG80001reservoir
650 mMpotassium phosphate1reservoirpH7.5
70.5 %1reservoirNaN3

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 28861

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Processing

Software
NameClassification
UCSD-systemdata collection
UCSD-systemdata reduction
X-PLORmodel building
X-PLORrefinement
UCSD-systemdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 6FAB

6fab


Resolution: 1.9→6 Å / Isotropic thermal model: Isotropic / Cross valid method: not applied / σ(F): 2 / Stereochemistry target values: Engh & Huber /
RfactorNum. reflection
Rwork0.196 -
obs0.196 28861
Refinement stepCycle: LAST / Resolution: 1.9→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3335 0 0 112 3447
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.013
X-RAY DIFFRACTIONp_angle_d1.911
X-RAY DIFFRACTIONc_dihedral_angle_d28.887
X-RAY DIFFRACTIONc_improper_angle_d1.674
LS refinement shellResolution: 1.9→1.98 Å /
RfactorNum. reflection
Rwork0.276 -
Rfree-0
obs-2518
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Lowest resolution: 6 Å / σ(F): 2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONx_bond_d
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_improper_angle_d
LS refinement shell
*PLUS
Rfactor Rwork: 0.276 / Rfactor obs: 0.276

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