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- PDB-1lo3: Retro-Diels-Alderase Catalytic Antibody: Product Analogue -

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Basic information

Entry
Database: PDB / ID: 1lo3
TitleRetro-Diels-Alderase Catalytic Antibody: Product Analogue
Components
  • If kappa light chain
  • Ig gamma 2a heavy chain
KeywordsIMMUNE SYSTEM / Fab / catalytic antibody / product complex
Function / homology
Function and homology information


immunoglobulin complex / adaptive 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
3-(10-METHYL-ANTHRACEN-9-YL)-PROPIONIC ACID / Kappa light chain C_region / Ighg protein / :
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 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 6, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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
Remark 999SEQUENCE At the time of processing, this sequence had 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)96,4766
Polymers95,9484
Non-polymers5292
Water1,63991
1
X: If kappa light chain
Y: Ig gamma 2a heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2383
Polymers47,9742
Non-polymers2641
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3750 Å2
ΔGint-30 kcal/mol
Surface area19870 Å2
MethodPISA
2
L: If kappa light chain
H: Ig gamma 2a heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2383
Polymers47,9742
Non-polymers2641
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3820 Å2
ΔGint-28 kcal/mol
Surface area19960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.384, 139.768, 84.860
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number4
Space group name H-MP1211

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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: Q99M37, UniProt: Q65ZC0*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: Q91Z05*PLUS
#3: Chemical ChemComp-AN1 / 3-(10-METHYL-ANTHRACEN-9-YL)-PROPIONIC ACID


Mass: 264.318 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H16O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 2.49 Å3/Da / Density % sol: 50.7 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 3
Details: PEG3350, pH 3.0, 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 Mcitric acid1reservoirpH3.0

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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: 2.3→30.5 Å / Num. obs: 39582 / % possible obs: 89.5 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 25 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 16.7
Reflection shellResolution: 2.3→2.42 Å / Rmerge(I) obs: 0.337 / Mean I/σ(I) obs: 3 / % possible all: 83.2
Reflection
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 30.5 Å / Num. measured all: 393333
Reflection shell
*PLUS
Highest resolution: 2.3 Å / % possible obs: 83.2 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
CNSrefinement
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→30.3 Å / Isotropic thermal model: GROUPED B-FACTORS / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER / Details: TWINNING LAW H, -K, -L TWINNING FRACTION 0.379
RfactorNum. reflectionSelection details
Rfree0.259 1782 RANDOM, BUT KEEPING TWIN- RELATED REFLECTIONS IN THE SAME SET
Rwork0.208 --
obs0.208 36347 -
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--6.325 Å20 Å20 Å2
2--4.509 Å20 Å2
3---1.816 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.47 Å0.38 Å
Refinement stepCycle: LAST / Resolution: 2.3→30.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6750 0 40 91 6881
Refine LS restraints NCSNCS model details: RESTRAIN
Refinement
*PLUS
Rfactor Rfree: 0.251 / Rfactor Rwork: 0.188
Solvent computation
*PLUS
Displacement parameters
*PLUS

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