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- PDB-1bz7: FAB FRAGMENT FROM MURINE ASCITES -

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Basic information

Entry
Database: PDB / ID: 1bz7
TitleFAB FRAGMENT FROM MURINE ASCITES
Components
  • PROTEIN (ANTIBODY R24 (HEAVY CHAIN))
  • PROTEIN (ANTIBODY R24 (LIGHT CHAIN))
KeywordsIMMUNE SYSTEM / ANTIBODY (FAB FRAGMENT)
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsKaminski, M.J. / Mackenzie, C.R. / Mooibroek, M.J. / Dahms, T.E.S. / Hirama, T. / Houghton, A.N. / Chapman, P.B. / Evans, 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 6, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Nov 10, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 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 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (ANTIBODY R24 (LIGHT CHAIN))
B: PROTEIN (ANTIBODY R24 (HEAVY CHAIN))


Theoretical massNumber of molelcules
Total (without water)45,7342
Polymers45,7342
Non-polymers00
Water23413
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3500 Å2
ΔGint-26 kcal/mol
Surface area18860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.800, 56.000, 80.000
Angle α, β, γ (deg.)90.00, 119.20, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody PROTEIN (ANTIBODY R24 (LIGHT CHAIN))


Mass: 22715.277 Da / Num. of mol.: 1 / Fragment: FAB / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#2: Antibody PROTEIN (ANTIBODY R24 (HEAVY CHAIN))


Mass: 23018.723 Da / Num. of mol.: 1 / Fragment: FAB / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H2O
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: 3.14 Å3/Da / Density % sol: 60.79 %
Crystal growpH: 7 / Details: pH 7.0
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: used to seeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.2 Mzinc acetate1reservoir
20.1 Msodium cacodylate1reservoir
323 %PEG80001reservoir

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Data collection

DiffractionMean temperature: 300 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: MARRESEARCH / 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: 2.5→6 Å / Num. obs: 18143 / % possible obs: 94 % / Observed criterion σ(I): 3 / Redundancy: 4.4 % / Rsym value: 0.05
Reflection
*PLUS
Num. measured all: 79380 / Rmerge(I) obs: 0.05

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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 / Resolution: 2.5→6 Å / σ(F): 2
RfactorNum. reflection% reflection
Rwork0.162 --
obs0.162 18143 94 %
Refinement stepCycle: LAST / Resolution: 2.5→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3219 0 0 13 3232
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
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_deg1.35
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: 2.5 Å / Lowest resolution: 6 Å / σ(F): 2
Solvent computation
*PLUS
Displacement parameters
*PLUS

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