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- PDB-1lo4: Retro-Diels-Alderase Catalytic antibody 9D9 -

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Basic information

Entry
Database: PDB / ID: 1lo4
TitleRetro-Diels-Alderase Catalytic antibody 9D9
Components
  • If kappa light chain
  • Ig gamma 2a heavy chain
KeywordsIMMUNE SYSTEM / Fab / catalytic antibody / retro-Deils-Alderase
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
Kappa light chain C_region / Ighg protein / :
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 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 1.3Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.4Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
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
L: If kappa light chain
H: Ig gamma 2a heavy chain


Theoretical massNumber of molelcules
Total (without water)47,6512
Polymers47,6512
Non-polymers00
Water34219
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3810 Å2
ΔGint-25 kcal/mol
Surface area19650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.703, 80.355, 125.103
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 23994.537 Da / Num. of mol.: 1 / 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: 23656.791 Da / Num. of mol.: 1 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 2.57 Å3/Da / Density % sol: 52.09 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: PEG4000, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
115 mg/mlFab1drop
210 mMTris-HCl1droppH7.8
30.2 Mammonium sulfate1reservoir
40.1 Msodium acetate1reservoirpH4.6
530 %(w/v)PEG40001reservoir

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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: Oct 10, 1999 / Details: Yale mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→40 Å / Num. obs: 19718 / % possible obs: 99 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 45 Å2 / Rmerge(I) obs: 0.027 / Net I/σ(I): 30.2
Reflection shellResolution: 2.4→2.53 Å / Rmerge(I) obs: 0.116 / Mean I/σ(I) obs: 10.6 / % possible all: 98.3
Reflection
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 40 Å / % possible obs: 99 % / Num. measured all: 182312
Reflection shell
*PLUS
Highest resolution: 2.4 Å / % possible obs: 98.3 %

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Processing

Software
NameVersionClassification
REFMAC5refinement
SCALAdata scaling
CNSrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→38.35 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.865 / SU B: 9.885 / SU ML: 9.885 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.466 / ESU R Free: 0.32 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.3079 1053 5.3 %RANDOM
Rwork0.23532 ---
all0.2391 18630 --
obs0.23917 18630 100 %-
Solvent computationShrinkage radii: 0.8 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 26.887 Å2
Baniso -1Baniso -2Baniso -3
1-3.18 Å20 Å20 Å2
2---0.74 Å20 Å2
3----2.44 Å2
Refinement stepCycle: LAST / Resolution: 2.4→38.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3352 0 0 19 3371
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0213435
X-RAY DIFFRACTIONr_angle_refined_deg1.9061.9484681
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9343435
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.84415597
X-RAY DIFFRACTIONr_chiral_restr0.1640.2537
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022575
X-RAY DIFFRACTIONr_nbd_refined0.2860.31532
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.5353
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3410.353
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.270.51
X-RAY DIFFRACTIONr_mcbond_it2.7281.52173
X-RAY DIFFRACTIONr_mcangle_it4.00823531
X-RAY DIFFRACTIONr_scbond_it5.4652.51262
X-RAY DIFFRACTIONr_scangle_it6.6831150
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.391 68
Rwork0.269 1352
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.13412.7516-1.73113.3573-1.02163.40980.16220.35790.19740.27480.16860.3046-0.3744-0.2862-0.33080.06870.08560.04390.11260.03630.08679.2355-44.4279-60.5643
22.24951.43910.11373.7050.44182.3294-0.07020.1265-0.1038-0.32810.0609-0.22620.18190.05760.00930.14460.03370.0070.09710.0210.083296.8031-51.1445-89.5422
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1LA1 - 1121 - 112
2X-RAY DIFFRACTION1HB1 - 1191 - 119
3X-RAY DIFFRACTION2LA113 - 217113 - 217
4X-RAY DIFFRACTION2HB120 - 220120 - 220
Refinement
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 40 Å / Rfactor Rfree: 0.315 / Rfactor Rwork: 0.25
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 2.46 Å

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