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- PDB-1lo2: Retro-Diels-Alderase Catalytic Antibody -

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Basic information

Entry
Database: PDB / ID: 1lo2
TitleRetro-Diels-Alderase Catalytic Antibody
Components
  • If kappa light chain
  • Ig gamma 2a heavy chain
KeywordsIMMUNE SYSTEM / catalytic antibody / Fab / retro-Diels-Alderase
Function / homology
Function and homology information


Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain ...Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / 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
Chem-OX1 / Kappa light chain C_region / Ighg protein / :
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 6, 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 1.3Jul 21, 2021Group: Derived calculations / Refinement description / Category: refine / struct_sheet / struct_site
Item: _refine.ls_percent_reflns_obs / _struct_sheet.number_strands ..._refine.ls_percent_reflns_obs / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999 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)96,5406
Polymers95,9484
Non-polymers5932
Water2,522140
1
X: If kappa light chain
Y: Ig gamma 2a heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2703
Polymers47,9742
Non-polymers2961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4530 Å2
ΔGint-28 kcal/mol
Surface area19220 Å2
MethodPISA
2
L: If kappa light chain
H: Ig gamma 2a heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2703
Polymers47,9742
Non-polymers2961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4580 Å2
ΔGint-27 kcal/mol
Surface area19320 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

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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-OX1 / [2'-CARBOXYLETHYL]-10-METHYL-ANTHRACENE ENDOPEROXIDE


Mass: 296.317 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H16O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 140 / Source method: isolated from a natural source / Formula: H2O

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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: 9
Details: PEG3350, pH 9.0, 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 Mglycine1reservoir
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: 2→30.8 Å / Num. obs: 64582 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 28 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 26.9
Reflection shellResolution: 2→2.11 Å / Rmerge(I) obs: 0.138 / Mean I/σ(I) obs: 7.3 / % possible all: 97.5
Reflection
*PLUS
Num. measured all: 721745
Reflection shell
*PLUS
Highest resolution: 2 Å / % possible obs: 97.5 %

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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→30.8 Å / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.248 3014 -random, but twin-related reflections are in the same set, i.e. either working or test
Rwork0.21 ---
all-64582 --
obs-63992 99.5 %-
Displacement parametersBiso mean: 19.5 Å2
Baniso -1Baniso -2Baniso -3
1--4.49 Å20 Å20 Å2
2--2.26 Å20 Å2
3---2.23 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.25 Å
Luzzati d res low-30 Å
Luzzati sigma a0.39 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 2→30.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6750 0 44 140 6934
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_d1.45
LS refinement shellResolution: 2→2.07 Å
RfactorNum. reflection
Rfree0.3036 236
Rwork0.2767 -
obs-6225
Refinement
*PLUS
Highest resolution: 2 Å / Rfactor Rwork: 0.2083
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.45

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