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- PDB-1f3d: CATALYTIC ANTIBODY 4B2 IN COMPLEX WITH ITS AMIDINIUM HAPTEN. -

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Basic information

Entry
Database: PDB / ID: 1f3d
TitleCATALYTIC ANTIBODY 4B2 IN COMPLEX WITH ITS AMIDINIUM HAPTEN.
Components(CATALYTIC ANTIBODY 4B2) x 2
KeywordsIMMUNE SYSTEM / catalytic antibody / amidinium / haptenic charge
Function / homology
Function and homology information


: / 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 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-TPM / If kappa light chain
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsGolinelli-Pimpaneau, B. / Goncalves, O. / Dintinger, T. / Blanchard, D. / Knossow, M. / Tellier, C.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2000
Title: Structural evidence for a programmed general base in the active site of a catalytic antibody.
Authors: Golinelli-Pimpaneau, B. / Goncalves, O. / Dintinger, T. / Blanchard, D. / Knossow, M. / Tellier, C.
#1: Journal: BIOCHEM.J. / Year: 2000
Title: Mechanism of an Antibody-Catalysed Allylic Isomerization.
Authors: Goncalves, O. / Dintinger, T. / Lebreton, J. / Blanchard, D. / Tellier, C.
History
DepositionJun 2, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 13, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 4, 2012Group: Version format compliance
Revision 1.4Oct 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: CATALYTIC ANTIBODY 4B2
H: CATALYTIC ANTIBODY 4B2
J: CATALYTIC ANTIBODY 4B2
K: CATALYTIC ANTIBODY 4B2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,5037
Polymers94,9984
Non-polymers5053
Water5,549308
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.000, 87.200, 128.800
Angle α, β, γ (deg.)90.00, 97.60, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody CATALYTIC ANTIBODY 4B2


Mass: 24206.977 Da / Num. of mol.: 2 / Fragment: LIGHT CHAIN - FAB FRAGMENT / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Tissue fraction: ASCITES FLUID / References: UniProt: A2NHM3*PLUS
#2: Antibody CATALYTIC ANTIBODY 4B2


Mass: 23292.092 Da / Num. of mol.: 2 / Fragment: HEAVY CHAIN - FAB FRAGMENT / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Tissue fraction: ASCITES FLUID
#3: Chemical ChemComp-TPM / 2-(4-AMINOBENZYLAMINO)-3,4,5,6-TETRAHYDROPYRIDINIUM


Mass: 204.291 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H18N3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 308 / 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: 2.64 Å3/Da / Density % sol: 53.33 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5
Details: PEG 4000, ammonium sulfate, acetate, stontium chloride, glycerol, dioxan, pH 5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
116 %(v/v)PEG40001reservoir
23 %(v/v)dioxane1reservoir
320 %(v/v)glycerol1reservoir
40.2 Mammonium sulfate1reservoir
55 mMstrontium chloride1reservoir
620 mMsodium acetate1reservoir
70.25 mMhapten1drop
811.6 mg/mlFab1drop
90.15 M1dropNaCl
100.05 %1dropNaN3

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.9607
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 29, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9607 Å / Relative weight: 1
ReflectionResolution: 1.87→20 Å / Num. all: 81391 / Num. obs: 79647 / % possible obs: 98 % / Observed criterion σ(I): -3 / Redundancy: 1.84 % / Biso Wilson estimate: 24.15 Å2 / Rmerge(I) obs: 0.039 / Net I/σ(I): 20
Reflection shellResolution: 1.87→1.9 Å / Redundancy: 1.87 % / Rmerge(I) obs: 0.201 / Mean I/σ(I) obs: 3.3 / Num. unique all: 3755 / % possible all: 94.9
Reflection
*PLUS
Num. measured all: 155936
Reflection shell
*PLUS
% possible obs: 94.9 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.87→20 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.218 7975 -RANDOM
Rwork0.198 ---
all-79627 --
obs-79342 97.5 %-
Refinement stepCycle: LAST / Resolution: 1.87→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6600 0 35 308 6943
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.411
X-RAY DIFFRACTIONc_bond_d0.006
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / σ(F): 2 / % reflection Rfree: 10 % / Rfactor obs: 0.198
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Highest resolution: 1.87 Å / Lowest resolution: 1.9 Å / Rfactor Rfree: 0.281 / Rfactor obs: 0.274

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