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- PDB-1r24: FAB FROM MURINE IGG3 KAPPA -

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Basic information

Entry
Database: PDB / ID: 1r24
TitleFAB FROM MURINE IGG3 KAPPA
Components
  • PROTEIN (IGG3-KAPPA ANTIBODY (HEAVY CHAIN))
  • PROTEIN (IGG3-KAPPA ANTIBODY (LIGHT CHAIN))
KeywordsIMMUNE SYSTEM / PRELIMINARY
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsEvans, S.V.
CitationJournal: J.Biol.Chem. / Year: 1999
Title: The role of homophilic binding in anti-tumor antibody R24 recognition of molecular surfaces. Demonstration of an intermolecular beta-sheet interaction between vh domains.
Authors: Kaminski, M.J. / MacKenzie, C.R. / Mooibroek, M.J. / Dahms, T.E. / Hirama, T. / Houghton, A.N. / Chapman, P.B. / Evans, S.V.
History
DepositionNov 5, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Nov 8, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Dec 7, 2011Group: Database references
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.6Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (IGG3-KAPPA ANTIBODY (LIGHT CHAIN))
B: PROTEIN (IGG3-KAPPA ANTIBODY (HEAVY CHAIN))
C: PROTEIN (IGG3-KAPPA ANTIBODY (LIGHT CHAIN))
D: PROTEIN (IGG3-KAPPA ANTIBODY (HEAVY CHAIN))


Theoretical massNumber of molelcules
Total (without water)91,7924
Polymers91,7924
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: PROTEIN (IGG3-KAPPA ANTIBODY (LIGHT CHAIN))
D: PROTEIN (IGG3-KAPPA ANTIBODY (HEAVY CHAIN))


Theoretical massNumber of molelcules
Total (without water)45,8962
Polymers45,8962
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3470 Å2
ΔGint-24 kcal/mol
Surface area19190 Å2
MethodPISA, PQS
3
A: PROTEIN (IGG3-KAPPA ANTIBODY (LIGHT CHAIN))
B: PROTEIN (IGG3-KAPPA ANTIBODY (HEAVY CHAIN))


Theoretical massNumber of molelcules
Total (without water)45,8962
Polymers45,8962
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3390 Å2
ΔGint-23 kcal/mol
Surface area19290 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)139.240, 82.070, 73.580
Angle α, β, γ (deg.)90.00, 94.13, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody PROTEIN (IGG3-KAPPA ANTIBODY (LIGHT CHAIN))


Mass: 22827.256 Da / Num. of mol.: 2 / Fragment: FAB / Source method: isolated from a natural source / Details: FROM ASCITES / Source: (natural) Mus musculus (house mouse)
#2: Antibody PROTEIN (IGG3-KAPPA ANTIBODY (HEAVY CHAIN))


Mass: 23068.889 Da / Num. of mol.: 2 / Fragment: FAB / Source method: isolated from a natural source / Details: FROM ASCITES / Source: (natural) Mus musculus (house mouse)
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: 4.57 Å3/Da / Density % sol: 73.06 %
Crystal growpH: 7 / Details: pH 7.0
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
123 %PEG80001reservoir
20.2 Mzinc acetate1reservoir
30.1 Msodium cacodylate1reservoir

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Data collection

DiffractionMean temperature: 270 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.1→6 Å / Num. obs: 26595 / % possible obs: 92 % / Observed criterion σ(I): 0 / Redundancy: 2.2 % / Biso Wilson estimate: 35.3 Å2 / Rsym value: 0.075
Reflection
*PLUS
Num. measured all: 58762 / Rmerge(I) obs: 0.075

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
MERLOTphasing
X-PLORmodel building
X-PLOR3.1refinement
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: FAB FROM YST9.1

Resolution: 3.1→6 Å / σ(F): 0
RfactorNum. reflection% reflection
Rwork0.245 --
obs0.245 26595 92 %
Displacement parametersBiso mean: 28.4 Å2
Refinement stepCycle: LAST / Resolution: 3.1→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6458 0 0 0 6458
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.022
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_deg3.8
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
Xplor fileSerial no: 1 / Param file: PARAM19X.PRO / Topol file: TOPH19X.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 3.1 Å / Lowest resolution: 6 Å / σ(F): 0 / Rfactor Rfree: 0.334
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 28.4 Å2
Refine LS restraints
*PLUS
Type: x_angle_deg / Dev ideal: 3.8

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