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- PDB-6fab: THREE-DIMENSIONAL STRUCTURE OF MURINE ANTI-P-AZOPHENYLARSONATE FA... -

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Basic information

Entry
Database: PDB / ID: 6fab
TitleTHREE-DIMENSIONAL STRUCTURE OF MURINE ANTI-P-AZOPHENYLARSONATE FAB 36-71. 1. X-RAY CRYSTALLOGRAPHY, SITE-DIRECTED MUTAGENESIS, AND MODELING OF THE COMPLEX WITH HAPTEN
Components
  • IGG1-KAPPA 36-71 FAB (HEAVY CHAIN)
  • IGG1-KAPPA 36-71 FAB (LIGHT CHAIN)
KeywordsIMMUNOGLOBULIN
Function / homology
Function and homology information


B cell differentiation / 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 speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsStrong, R.K. / Rose, D.R. / Petsko, G.A. / Sharon, J. / Margolies, M.N.
Citation
Journal: Biochemistry / Year: 1991
Title: Three-dimensional structure of murine anti-p-azophenylarsonate Fab 36-71. 1. X-ray crystallography, site-directed mutagenesis, and modeling of the complex with hapten.
Authors: Strong, R.K. / Campbell, R. / Rose, D.R. / Petsko, G.A. / Sharon, J. / Margolies, M.N.
#1: Journal: Biochemistry / Year: 1991
Title: Three-Dimensional Structure of Murine Anti-P-Azophenylarsonate Fab 36-71. 2. Structural Basis of Hapten Binding and Idiotypy
Authors: Strong, R.K. / Petsko, G.A. / Sharon, J. / Margolies, M.N.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1990
Title: Crystal Structure of the Antigen-Binding Fragment of the Murine Anti-Arsonate Monoclonal Antibody 36-71 at 2.9 Angstroms Resolution
Authors: Rose, D.R. / Strong, R.K. / Margolies, M.N. / Gefter, M.L. / Petsko, G.A.
History
DepositionJan 17, 1991Processing site: BNL
Revision 1.0Jan 15, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
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: IGG1-KAPPA 36-71 FAB (LIGHT CHAIN)
H: IGG1-KAPPA 36-71 FAB (HEAVY CHAIN)


Theoretical massNumber of molelcules
Total (without water)47,5172
Polymers47,5172
Non-polymers00
Water1,26170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3970 Å2
ΔGint-26 kcal/mol
Surface area19210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.130, 73.050, 46.780
Angle α, β, γ (deg.)90.00, 104.48, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: RESIDUES PRO L 8, PRO L 95, PRO L 141, PRO H 155, PRO H 157, AND PRO H 197 ARE CIS PROLINES.

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Components

#1: Antibody IGG1-KAPPA 36-71 FAB (LIGHT CHAIN)


Mass: 23644.014 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / References: UniProt: P01837
#2: Antibody IGG1-KAPPA 36-71 FAB (HEAVY CHAIN)


Mass: 23872.635 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / 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: 2.34 Å3/Da / Density % sol: 47.35 %

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Data collection

Reflection
*PLUS
Highest resolution: 1.7 Å / Rmerge(I) obs: 0.0664

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Processing

Software
NameClassification
X-PLORmodel building
PROLSQrefinement
X-PLORrefinement
X-PLORphasing
RefinementRfactor obs: 0.209 / Highest resolution: 1.9 Å
Refinement stepCycle: LAST / Highest resolution: 1.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3339 0 0 70 3409
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.019
X-RAY DIFFRACTIONp_angle_d3.99
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONx_bond_d
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_deg
X-RAY DIFFRACTIONx_planar_d
X-RAY DIFFRACTIONx_plane_restr
X-RAY DIFFRACTIONx_chiral_restr
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scangle_it

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