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- PDB-1dsf: THE CRYSTAL STRUCTURE OF THE DISULFIDE-STABILIZED FV FRAGMENT OF ... -

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Basic information

Entry
Database: PDB / ID: 1dsf
TitleTHE CRYSTAL STRUCTURE OF THE DISULFIDE-STABILIZED FV FRAGMENT OF ANTICANCER ANTIBODY B1: CONFORMATIONAL INFLUENCE OF AN ENGINEERED DISULFIDE BOND
Components(ANTICANCER ANTIBODY B1) x 2
KeywordsIMMUNOGLOBULIN / MONOCLONAL ANTIBODY / ANTITUMOR
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / :
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsAlmog, O. / Gilliland, G.L.
CitationJournal: Proteins / Year: 1998
Title: Crystal structure of the disulfide-stabilized Fv fragment of anticancer antibody B1: conformational influence of an engineered disulfide bond.
Authors: Almog, O. / Benhar, I. / Vasmatzis, G. / Tordova, M. / Lee, B. / Pastan, I. / Gilliland, G.L.
History
DepositionMay 4, 1997Processing site: BNL
Revision 1.0May 13, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details
Revision 1.4Oct 30, 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
L: ANTICANCER ANTIBODY B1
H: ANTICANCER ANTIBODY B1


Theoretical massNumber of molelcules
Total (without water)25,4732
Polymers25,4732
Non-polymers00
Water3,243180
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1790 Å2
ΔGint-17 kcal/mol
Surface area10220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.100, 80.100, 138.200
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Antibody ANTICANCER ANTIBODY B1 / B1DSFV


Mass: 12223.854 Da / Num. of mol.: 1 / Fragment: FV / Mutation: CHAIN L, A100C, CHAIN H, R44C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Strain: BALB/C / Cell line: BL21 / Organ: SPLEEN / Plasmid: PB1VHR44C-STOP\ PB1VL A100C-STOP / Species (production host): Escherichia coli / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: PIR: B41940
#2: Antibody ANTICANCER ANTIBODY B1 / B1DSFV


Mass: 13248.775 Da / Num. of mol.: 1 / Fragment: FV / Mutation: CHAIN L, A100C, CHAIN H, R44C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Strain: BALB/C / Cell line: BL21 / Organ: SPLEEN / Plasmid: PB1VHR44C-STOP\ PB1VL A100C-STOP / Species (production host): Escherichia coli / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / 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: 2.6 Å3/Da / Density % sol: 54 %
Crystal growpH: 7 / Details: 1.6M HEPES PH-7.0
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
116 mg/mlprotein1drop
210 mMHEPES-HCl1drop
31.6 Mammonium sulfate1reservoir
40.1 MHEPES1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Dec 1, 1995
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.12→57.8 Å / Num. obs: 14289 / % possible obs: 92 % / Observed criterion σ(I): 0 / Redundancy: 6 % / Rsym value: 0.108 / Net I/σ(I): 6.8
Reflection shellResolution: 2.12→2.2 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 1.5 / Rsym value: 0.2644 / % possible all: 58
Reflection
*PLUS
Num. all: 15524 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.066

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Processing

Software
NameVersionClassification
XENGENdata collection
XENGENdata reduction
X-PLOR3.1model building
X-PLOR3.1refinement
XENGENdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1IGG

1igg


Resolution: 2→8 Å / σ(F): 2 /
RfactorNum. reflection
Rwork0.182 -
obs0.182 11443
Refinement stepCycle: LAST / Resolution: 2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1791 0 0 180 1971
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
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_deg2.74
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 file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPH19.PEP
X-RAY DIFFRACTION2PARAM.H2OTOPHCSDX.PRO
X-RAY DIFFRACTION3TOPOL.H2O

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