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- PDB-1mcp: PHOSPHOCHOLINE BINDING IMMUNOGLOBULIN FAB MC/PC603. AN X-RAY DIFF... -

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Basic information

Entry
Database: PDB / ID: 1mcp
TitlePHOSPHOCHOLINE BINDING IMMUNOGLOBULIN FAB MC/PC603. AN X-RAY DIFFRACTION STUDY AT 2.7 ANGSTROMS
Components
  • IGA-KAPPA MCPC603 FAB (HEAVY CHAIN)
  • IGA-KAPPA MCPC603 FAB (LIGHT CHAIN)
KeywordsIMMUNOGLOBULIN
Function / homology
Function and homology information


immunoglobulin complex / immunoglobulin mediated immune response / antigen binding / extracellular region
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 / 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 / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / Ig heavy chain V region M603
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / Resolution: 2.7 Å
AuthorsSatow, Y. / Cohen, G.H. / Padlan, E.A. / Davies, D.R.
Citation
Journal: J.Mol.Biol. / Year: 1986
Title: Phosphocholine binding immunoglobulin Fab McPC603. An X-ray diffraction study at 2.7 A.
Authors: Satow, Y. / Cohen, G.H. / Padlan, E.A. / Davies, D.R.
#1: Journal: Mol.Immunol. / Year: 1981
Title: Kappa Chain Structure from a Crystallized Murine Fab(Prime). Role of Joining Segment in Hapten Binding
Authors: Rudikoff, S. / Satow, Y. / Padlan, E. / Davies, D. / Potter, M.
#2: Journal: Contemp.Top.Mol.Immunol. / Year: 1975
Title: Immunoglobulin Structures at High Resolution
Authors: Davies, D.R. / Padlan, E.A. / Segal, D.M.
#3: Journal: The Immune System. Genes,Receptors,Signals. Proceedings of the 1974 I.C.N.-U.C.L.A. Symposium on Molecular Biology
Year: 1974
Title: The Three-Dimensional Structure of the Antigen Binding Site of Mc/Pc 603 Protein
Authors: Padlan, E.A. / Segal, D.M. / Cohen, G.H. / Davies, D.R. / Rudikoff, S. / Potter, M.
#4: Journal: Proc.Natl.Acad.Sci.USA / Year: 1974
Title: The Three-Dimensional Structure of a Phosphorylcholine-Binding Mouse Immunoglobulin Fab and the Nature of the Antigen Binding Site
Authors: Segal, D.M. / Padlan, E.A. / Cohen, G.H. / Rudikoff, S. / Potter, M. / Davies, D.R.
#5: Journal: Nature New Biol. / Year: 1973
Title: Structure at 4.5 Angstroms Resolution of a Phosphorylcholine-Binding Fab
Authors: Padlan, E.A. / Segal, D.M. / Spande, T.F. / Davies, D.R. / Rudikoff, S. / Potter, M.
#6: Journal: Proc.Natl.Acad.Sci.USA / Year: 1972
Title: Crystals of Phosphorylcholine-Binding Fab-Fragments from Mouse Myeloma Proteins. Preparation and X-Ray Analysis
Authors: Rudikoff, S. / Potter, M. / Segal, D.M. / Padlan, E.A. / Davies, D.R.
History
DepositionJul 9, 1984Processing site: BNL
Revision 1.0Jan 2, 1985Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 2.0Jul 26, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Other
Category: atom_site / atom_sites ...atom_site / atom_sites / database_2 / database_PDB_matrix / pdbx_database_remark / pdbx_database_status / pdbx_validate_main_chain_plane / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_symm_contact / pdbx_validate_torsion / struct_conn / struct_ref_seq_dif / struct_site
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[1][2] / _atom_sites.fract_transf_matrix[2][1] / _atom_sites.fract_transf_matrix[2][2] / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _database_PDB_matrix.origx[1][1] / _database_PDB_matrix.origx[1][2] / _database_PDB_matrix.origx[2][1] / _database_PDB_matrix.origx[2][2] / _pdbx_database_status.process_site / _pdbx_validate_main_chain_plane.improper_torsion_angle / _pdbx_validate_rmsd_angle.angle_deviation / _pdbx_validate_rmsd_angle.angle_value / _pdbx_validate_symm_contact.dist / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _struct_conn.pdbx_dist_value / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Details: Coordinates and associated ncs operations (if present) transformed into standard crystal frame
Provider: repository / Type: Remediation
Revision 2.1Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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: IGA-KAPPA MCPC603 FAB (LIGHT CHAIN)
H: IGA-KAPPA MCPC603 FAB (HEAVY CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5293
Polymers48,4332
Non-polymers961
Water2,486138
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3720 Å2
ΔGint-39 kcal/mol
Surface area19700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)162.531, 162.531, 60.719
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Atom site foot note1: FOR RESIDUES 28-37 AND 162-163 OF THE LIGHT CHAIN AND RESIDUE 202 OF THE HEAVY CHAIN, THE DENSITY WAS POOR. THESE RESIDUES WERE BUILT MAINLY BY STEREOCHEMISTRY.
2: RESIDUES PRO L 8, PRO L 101, PRO L 147, PRO H 143, PRO H 155 ARE CIS PROLINES.

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Components

#1: Antibody IGA-KAPPA MCPC603 FAB (LIGHT CHAIN)


Mass: 24113.584 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / References: GenBank: 208622
#2: Antibody IGA-KAPPA MCPC603 FAB (HEAVY CHAIN)


Mass: 24319.266 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / References: UniProt: P01789
#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.: 138 / 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

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Sample preparation

CrystalDensity Matthews: 4.78 Å3/Da / Density % sol: 74.25 %
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
243 %satammonium sulfate1reservior
1protein1drop

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 10 Å / Num. obs: 24235 / Num. measured all: 147706

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Processing

RefinementRfactor Rwork: 0.225 / Highest resolution: 2.7 Å
Refinement stepCycle: LAST / Highest resolution: 2.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3401 0 5 138 3544
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.02
X-RAY DIFFRACTIONo_bond_d_na
X-RAY DIFFRACTIONo_bond_d_prot
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_d_na
X-RAY DIFFRACTIONo_angle_d_prot
X-RAY DIFFRACTIONo_angle_deg3.5
X-RAY DIFFRACTIONo_angle_deg_na
X-RAY DIFFRACTIONo_angle_deg_prot
X-RAY DIFFRACTIONo_dihedral_angle_d
X-RAY DIFFRACTIONo_dihedral_angle_d_na
X-RAY DIFFRACTIONo_dihedral_angle_d_prot
X-RAY DIFFRACTIONo_improper_angle_d
X-RAY DIFFRACTIONo_improper_angle_d_na
X-RAY DIFFRACTIONo_improper_angle_d_prot
X-RAY DIFFRACTIONo_mcbond_it
X-RAY DIFFRACTIONo_mcangle_it
X-RAY DIFFRACTIONo_scbond_it
X-RAY DIFFRACTIONo_scangle_it
Refinement
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 8 Å / Num. reflection obs: 23737 / Rfactor obs: 0.225
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_angle_d3.5
X-RAY DIFFRACTIONo_improper_angle_d
X-RAY DIFFRACTIONo_planar_d0.037
X-RAY DIFFRACTIONo_plane_restr0.027
X-RAY DIFFRACTIONo_chiral_restr0.257
X-RAY DIFFRACTIONo_mcbond_it0.5
X-RAY DIFFRACTIONo_scbond_it0.4
X-RAY DIFFRACTIONo_mcangle_it1
X-RAY DIFFRACTIONo_scangle_it0.7

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