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- PDB-1ucb: STRUCTURE OF UNCOMPLEXED FAB COMPARED TO COMPLEX (1CLY, 1CLZ) -

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Basic information

Entry
Database: PDB / ID: 1ucb
TitleSTRUCTURE OF UNCOMPLEXED FAB COMPARED TO COMPLEX (1CLY, 1CLZ)
Components(CHIMERIC HUMAN/MOUSE IGG FAB FRAGMENT BR96) x 2
KeywordsIMMUNOGLOBULIN / FAB / ANTIBODY / ANTI-TUMOR / CHIMERA
Function / homology
Function and homology information


IgD immunoglobulin complex / IgA immunoglobulin complex / IgM immunoglobulin complex / IgE immunoglobulin complex / CD22 mediated BCR regulation / IgG immunoglobulin complex / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin mediated immune response ...IgD immunoglobulin complex / IgA immunoglobulin complex / IgM immunoglobulin complex / IgE immunoglobulin complex / CD22 mediated BCR regulation / IgG immunoglobulin complex / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin mediated immune response / FCGR activation / Role of LAT2/NTAL/LAB on calcium mobilization / Role of phospholipids in phagocytosis / Scavenging of heme from plasma / antigen binding / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Regulation of Complement cascade / Cell surface interactions at the vascular wall / B cell receptor signaling pathway / FCGR3A-mediated phagocytosis / FCERI mediated MAPK activation / Regulation of actin dynamics for phagocytic cup formation / FCERI mediated NF-kB activation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / blood microparticle / adaptive immune response / Potential therapeutics for SARS / immune response / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
: / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold ...: / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Immunoglobulin kappa constant
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSheriff, S. / Bajorath, J.
Citation
Journal: J.Mol.Biol. / Year: 1996
Title: X-ray structure of the uncomplexed anti-tumor antibody BR96 and comparison with its antigen-bound form.
Authors: Sheriff, S. / Chang, C.Y. / Jeffrey, P.D. / Bajorath, J.
#1: Journal: J.Mol.Biol. / Year: 1994
Title: Crystallization and Preliminary X-Ray Analysis of the Monoclonal Anti-Tumor Antibody Br96 and its Complex with the Lewis Y Determinant
Authors: Chang, C.Y. / Jeffrey, P.D. / Bajorath, J. / Hellstrom, I. / Hellstrom, K.E. / Sheriff, S.
History
DepositionFeb 6, 1996Processing site: BNL
Revision 1.0Mar 12, 1997Provider: 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 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: CHIMERIC HUMAN/MOUSE IGG FAB FRAGMENT BR96
H: CHIMERIC HUMAN/MOUSE IGG FAB FRAGMENT BR96
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7833
Polymers47,6872
Non-polymers961
Water72140
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3720 Å2
ΔGint-37 kcal/mol
Surface area19410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.100, 174.300, 45.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Antibody CHIMERIC HUMAN/MOUSE IGG FAB FRAGMENT BR96 / CBR96 FAB / IMMUNOGLOBULIN


Mass: 24077.883 Da / Num. of mol.: 1
Fragment: MOUSE VH AND VL DOMAINS, HUMAN CL KAPPA AND CH1 IGG1 DOMAINS
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Description: MOUSE/HUMAN CHIMERA. MOUSE HYBRIDOMA PRODUCED BY FUSIONING BALB/C SPLEEN CELLS WITH 2X63-AG 8.653 MOUSE MYELOMA CELLS. HUMAN CONSTANT REGIONS INTRODUCED BY HOMOLOGOUS RECOMBINATION. CL ...Description: MOUSE/HUMAN CHIMERA. MOUSE HYBRIDOMA PRODUCED BY FUSIONING BALB/C SPLEEN CELLS WITH 2X63-AG 8.653 MOUSE MYELOMA CELLS. HUMAN CONSTANT REGIONS INTRODUCED BY HOMOLOGOUS RECOMBINATION. CL IS HUMAN KAPPA, CH1 IS HUMAN IGG1 DOMAIN.
Fragment: CL AND CH1 / Organ: SPLEEN / Cell (production host): SPLEEN, MYELOMA / Production host: Mus musculus (house mouse) / Strain (production host): BALB/C, 2X63-AG 8.653 / References: UniProt: P01834
#2: Antibody CHIMERIC HUMAN/MOUSE IGG FAB FRAGMENT BR96 / CBR96 FAB / IMMUNOGLOBULIN


Mass: 23609.449 Da / Num. of mol.: 1
Fragment: MOUSE VH AND VL DOMAINS, HUMAN CL KAPPA AND CH1 IGG1 DOMAINS
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Description: MOUSE/HUMAN CHIMERA. MOUSE HYBRIDOMA PRODUCED BY FUSIONING BALB/C SPLEEN CELLS WITH 2X63-AG 8.653 MOUSE MYELOMA CELLS. HUMAN CONSTANT REGIONS INTRODUCED BY HOMOLOGOUS RECOMBINATION. CL ...Description: MOUSE/HUMAN CHIMERA. MOUSE HYBRIDOMA PRODUCED BY FUSIONING BALB/C SPLEEN CELLS WITH 2X63-AG 8.653 MOUSE MYELOMA CELLS. HUMAN CONSTANT REGIONS INTRODUCED BY HOMOLOGOUS RECOMBINATION. CL IS HUMAN KAPPA, CH1 IS HUMAN IGG1 DOMAIN.
Fragment: CL AND CH1 / Organ: SPLEEN / Cell (production host): SPLEEN, MYELOMA / Production host: Mus musculus (house mouse) / Strain (production host): BALB/C, 2X63-AG 8.653
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE FAB LIGHT CHAIN (RESIDUES 1 - 214) HAS BEEN ASSIGNED CHAIN INDICATOR L. THE FAB HEAVY CHAIN ...THE FAB LIGHT CHAIN (RESIDUES 1 - 214) HAS BEEN ASSIGNED CHAIN INDICATOR L. THE FAB HEAVY CHAIN (RESIDUES 1 - 227) HAS BEEN ASSIGNED CHAIN INDICATOR H. THE FAB FRAGMENT IS NUMBERED BY THE CONVENTION OF E. KABAT (E.A. KABAT, T.T. WU, H.M. PERRY, K.S. GOTTESMAN, C. FOELLER SEQUENCES OF PROTEINS OF IMMUNOLOGICAL INTEREST, 5TH ED.,. (1991), NATIONAL INSTITUTES OF HEALTH, BETHESDA, MD.).

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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: 2.4 Å3/Da / Density % sol: 49 %
Crystal growpH: 4.6
Details: 0.1 M SODIUM ACETATE (PH 4.6), 0.1 M AMMONIUM SULFATE, 15 % PEG 8000.
Crystal grow
*PLUS
pH: 7 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
18 mg/mlprotein11
210 mMimidazole-HCl12

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: SIEMENS-NICOLET X100 / Detector: AREA DETECTOR / Date: Mar 1, 1993 / Details: MIRROR
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→36 Å / Num. obs: 14826 / % possible obs: 87 % / Observed criterion σ(I): 0 / Redundancy: 2 % / Rmerge(I) obs: 0.045 / Net I/σ(I): 16.1
Reflection shellResolution: 2.5→2.8 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.107 / Mean I/σ(I) obs: 4 / % possible all: 65
Reflection
*PLUS
Num. measured all: 29571
Reflection shell
*PLUS
Highest resolution: 2.53 Å / Lowest resolution: 2.8 Å / % possible obs: 65 %

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Processing

Software
NameVersionClassification
XDSdata scaling
XSCALEdata scaling
BRUTEmodel building
MERLOTphasing
X-PLOR3.1refinement
XDSdata reduction
BRUTEphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: FV OF 1CLZ WITH CDRS REMOVED 1CLY (HUMAN IGG1, HUMAN KAPPA) AND OF 1CLZ (MOUSE IGG3, MOUSE KAPPA)

1clz

1cly

1clz


Resolution: 2.5→8 Å / Cross valid method: EX POST FACTO / σ(F): 1
RfactorNum. reflection% reflection
Rfree0.276 -10 %
Rwork0.2 --
obs0.2 13731 87 %
Displacement parametersBiso mean: 29 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å
Refinement stepCycle: LAST / Resolution: 2.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3333 0 45 0 3378
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
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_deg1.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d28
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.4
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
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
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
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.4

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