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- PDB-2f19: THREE-DIMENSIONAL STRUCTURE OF TWO CRYSTAL FORMS OF FAB R19.9, FR... -

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Basic information

Entry
Database: PDB / ID: 2f19
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


IgG immunoglobulin complex / 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 / Immunoglobulins / 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Immunoglobulin kappa constant
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / Resolution: 2.8 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, 1992-
SupersessionOct 15, 1992ID: 1F19
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3790 Å2
ΔGint-26 kcal/mol
Surface area19520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.300, 80.800, 75.100
Angle α, β, γ (deg.)90.00, 96.00, 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)

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.76 Å3/Da / Density % sol: 55.49 %
Crystal grow
*PLUS
pH: 7.3 / Method: vapor diffusion, hanging drop / Details: took 8 from original paper: form II
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 %(v/v)PEG80001reservoir
20.2 Msodium chloride1reservior
33 mMsodium azide1reservoir
40.1 Mpottassium phosphate1reservoir

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Data collection

Reflection
*PLUS
Highest resolution: 2.5 Å / Num. obs: 16492 / Num. measured all: 4617 / Rmerge(I) obs: 0.08

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Processing

SoftwareName: X-PLOR / Classification: refinement
RefinementRfactor Rwork: 0.182 / Highest resolution: 2.8 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: 2.8 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_deg3.4
Refinement
*PLUS
Lowest resolution: 6 Å / Num. reflection obs: 10340 / σ(F): 3
Solvent computation
*PLUS
Displacement parameters
*PLUS

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