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- PDB-1lo0: Catalytic Retro-Diels-Alderase Transition State Analogue Complex -

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Basic information

Entry
Database: PDB / ID: 1lo0
TitleCatalytic Retro-Diels-Alderase Transition State Analogue Complex
Components
  • If kappa light chain
  • Ig gamma 2a heavy chain
KeywordsIMMUNE SYSTEM / catalytic antibody / Fab fragment
Function / homology
Function and homology information


positive regulation of B cell activation / phagocytosis, recognition / early endosome to late endosome transport / humoral immune response mediated by circulating immunoglobulin / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity / antibody-dependent cellular cytotoxicity / immunoglobulin complex, circulating / phagocytosis, engulfment / endosome to lysosome transport ...positive regulation of B cell activation / phagocytosis, recognition / early endosome to late endosome transport / humoral immune response mediated by circulating immunoglobulin / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity / antibody-dependent cellular cytotoxicity / immunoglobulin complex, circulating / phagocytosis, engulfment / endosome to lysosome transport / antigen processing and presentation / immunoglobulin mediated immune response / regulation of proteolysis / positive regulation of endocytosis / complement activation, classical pathway / antigen binding / multivesicular body / positive regulation of phagocytosis / B cell differentiation / response to bacterium / positive regulation of immune response / extracellular region / metal ion binding / plasma membrane
Similarity search - Function
: / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type ...: / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / 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
Chem-BC1 / If kappa light chain / Immunoglobulin kappa constant / Immunoglobulin heavy constant gamma 2A
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsHugot, M. / Reymond, J.L. / Baumann, U.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2002
Title: A structural basis for the activity of retro-Diels-Alder catalytic antibodies: evidence for a catalytic aromatic residue.
Authors: Hugot, M. / Bensel, N. / Vogel, M. / Reymond, M.T. / Stadler, B. / Reymond, J.L. / Baumann, U.
History
DepositionMay 5, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 999SEQUENCE At the time of processing, this sequence has not yet been deposited in a sequence database.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
X: If kappa light chain
Y: Ig gamma 2a heavy chain
L: If kappa light chain
H: Ig gamma 2a heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,6186
Polymers95,9484
Non-polymers6712
Water1,892105
1
X: If kappa light chain
Y: Ig gamma 2a heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3093
Polymers47,9742
Non-polymers3351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4590 Å2
ΔGint-28 kcal/mol
Surface area19210 Å2
MethodPISA
2
L: If kappa light chain
H: Ig gamma 2a heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3093
Polymers47,9742
Non-polymers3351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4620 Å2
ΔGint-28 kcal/mol
Surface area19290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.528, 140.095, 85.476
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain: (Details: RESTRAINED)

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Components

#1: Antibody If kappa light chain / Catalytic antibody 9D9


Mass: 24268.992 Da / Num. of mol.: 2 / Fragment: Fab fragment / Source method: isolated from a natural source
Details: The antibodies were isolated from hybridoma cells and Fab fragments were generated by papain digestion.
Source: (natural) Mus musculus (house mouse) / References: UniProt: P01837, UniProt: A2NHM3*PLUS
#2: Antibody Ig gamma 2a heavy chain


Mass: 23704.830 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: The antibodies were isolated from hybridoma cells and Fab fragments were generated by papain digestion.
Source: (natural) Mus musculus (house mouse) / References: UniProt: P01865
#3: Chemical ChemComp-BC1 / 3-{[(9-CYANO-9,10-DIHYDRO-10-METHYLACRIDIN-9-YL)CARBONYL]AMINO}PROPANOIC ACID


Mass: 335.357 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H17N3O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 51.34 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.8 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
116-20 mg/mlprotein1drop
20.6 mMhapten1drop
310 mMTris-HCl1droppH7.8
40.05 Mimidazole1reservoirpH7.0
512-18 %(w/v)PEG35501reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 1, 2000 / Details: Yale mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.77→30.3 Å / Num. obs: 78457 / % possible obs: 95.9 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 30 Å2 / Rmerge(I) obs: 0.051 / Rsym value: 0.051 / Net I/σ(I): 24.4
Reflection shellResolution: 1.77→1.85 Å / Rmerge(I) obs: 0.136 / Mean I/σ(I) obs: 9.9 / Rsym value: 0.136 / % possible all: 0.959
Reflection
*PLUS
Num. obs: 74192 / % possible obs: 81.7 % / Num. measured all: 1025225
Reflection shell
*PLUS
% possible obs: 95.9 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
CNSrefinement
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 28B4

28b4


Resolution: 2→30.3 Å / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
Details: CRYSTALS ARE PSEUDO-MEROHEDRALLY TWINNED TWINNING LAW H,-K,-L TWINNING FRACTION 0.3787
RfactorNum. reflection% reflectionSelection details
Rfree0.255 2879 -RANDOM, BUT KEEPING TWIN- RELATED REFLECTIONS IN THE SAME SET
Rwork0.206 ---
obs0.206 56868 93.3 %-
Solvent computationSolvent model: SOLVENT MASK / Bsol: 36.9 Å2 / ksol: 0.341 e/Å3
Displacement parametersBiso mean: 25.3 Å2
Baniso -1Baniso -2Baniso -3
1--3.209 Å20 Å20 Å2
2--0.06 Å20 Å2
3---3.149 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.25 Å
Luzzati d res low-30 Å
Luzzati sigma a0.25 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 2→30.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6756 0 50 106 6912
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.43
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d27.15
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.9
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2→2.07 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.314 231 -
Rwork0.286 5328 -
obs--87.8 %
Refinement
*PLUS
Rfactor Rfree: 0.256 / Rfactor Rwork: 0.204
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg27.15
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.9

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