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- PDB-1fai: THREE-DIMENSIONAL STRUCTURE OF TWO CRYSTAL FORMS OF FAB R19.9, FR... -

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Basic information

Entry
Database: PDB / ID: 1fai
TitleTHREE-DIMENSIONAL STRUCTURE OF TWO CRYSTAL FORMS OF FAB R19.9, FROM A MONOCLONAL ANTI-ARSONATE ANTIBODY
Components
  • IGG2B-KAPPA R19.9 FAB (HEAVY CHAIN)
  • IGG2B-KAPPA R19.9 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: 2.7 Å
AuthorsLascombe, M.B. / Alzari, P.M. / Poljak, R.J. / Nisonoff, A.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 1992
Title: Three-dimensional structure of two crystal forms of FabR19.9 from a monoclonal anti-arsonate antibody.
Authors: Lascombe, M.B. / Alzari, P.M. / Poljak, R.J. / Nisonoff, A.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1989
Title: Three-Dimensional Structure of Fab R19.9, A Monoclonal Murine Antibody Specific for the P-Azobenzenearsonate Group
Authors: Lascombe, M.B. / Alzari, P.M. / Boulot, G. / Saludjian, P. / Tougard, P. / Berek, C. / Haba, S. / Rosen, E.M. / Nisonoff, A. / Poljak, R.J.
#2: Journal: J.Biol.Chem. / Year: 1984
Title: Crystallization of the Fab Fragments of Monoclonal Anti-P-Azophenylarsonate Antibodies and Their Complexes with Haptens
Authors: Mariuzza, R.A. / Amit, A.G. / Boulot, G. / Saludjian, P. / Saul, F.A. / Tougard, P. / Poljak, R.J. / Conger, J. / Lamoyi, E. / Nisonoff, A.
History
DepositionMay 27, 1992Processing site: BNL
Revision 1.0Oct 15, 1992Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn
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_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_seq_id
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: IGG2B-KAPPA R19.9 FAB (LIGHT CHAIN)
H: IGG2B-KAPPA R19.9 FAB (HEAVY CHAIN)


Theoretical massNumber of molelcules
Total (without water)47,2562
Polymers47,2562
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3660 Å2
ΔGint-27 kcal/mol
Surface area19520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.000, 80.600, 75.200
Angle α, β, γ (deg.)90.00, 90.20, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: RESIDUES PRO L 95, PRO L 141, PRO H 158, AND PRO H 200 ARE CIS PROLINES.

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Components

#1: Antibody IGG2B-KAPPA R19.9 FAB (LIGHT CHAIN)


Mass: 23690.041 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 IGG2B-KAPPA R19.9 FAB (HEAVY CHAIN)


Mass: 23566.316 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse)
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: 2.69 Å3/Da / Density % sol: 54.31 %
Crystal grow
*PLUS
pH: 7.2 / Method: vapor diffusion / Details: took 9 from original paper
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115 mg/mlprotein1drop
20.02 Mpotassium phosphate1drop
325 %(w/v)PEG60001reservoir
40.1 Mpottassium phosphate1reservoir
53 mM1reservoirNaN3
60.3 M1reservoirNaCl

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.5 Å / Num. obs: 16492 / Observed criterion σ(I): 2 / Num. measured all: 41617 / Rmerge(I) obs: 0.08
Reflection shell
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 2.7 Å

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Processing

SoftwareName: X-PLOR / Classification: refinement
RefinementRfactor Rwork: 0.189 / Highest resolution: 2.7 Å
Details: THE POSITIONS OF MANY LOOPS IN THE CONSTANT REGION AND OF THE THIRD COMPLEMENTARITY-DETERMINING REGION OF THE HEAVY CHAIN (RESIDUES H 101 - H 109) ARE SOMEWHAT ARBITRARY, AS INDICATED BY ...Details: THE POSITIONS OF MANY LOOPS IN THE CONSTANT REGION AND OF THE THIRD COMPLEMENTARITY-DETERMINING REGION OF THE HEAVY CHAIN (RESIDUES H 101 - H 109) ARE SOMEWHAT ARBITRARY, AS INDICATED BY LARGE TEMPERATURE FACTORS.
Refinement stepCycle: LAST / Highest resolution: 2.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3320 0 0 0 3320
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
X-RAY DIFFRACTIONx_angle_deg3.5
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Lowest resolution: 6 Å / Num. reflection obs: 9855 / σ(F): 3 / Rfactor Rwork: 0.189
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_deg

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