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- PDB-1y18: Fab fragment of catalytic elimination antibody 34E4 E(H50)D mutan... -

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Basic information

Entry
Database: PDB / ID: 1y18
TitleFab fragment of catalytic elimination antibody 34E4 E(H50)D mutant in complex with hapten
Components
  • Catalytic antibody 34E4 heavy chain
  • Catalytic antibody 34E4 light chain
KeywordsIMMUNE SYSTEM / Immunoglobulin / Catalytic antibody / chimeric Fab / Hapten complex
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Chem-HAN
Function and homology information
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsDebler, E.W. / Ito, S. / Heine, A. / Wilson, I.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2005
Title: Structural origins of efficient proton abstraction from carbon by a catalytic antibody
Authors: Debler, E.W. / Ito, S. / Seebeck, F.P. / Heine, A. / Hilvert, D. / Wilson, I.A.
History
DepositionNov 17, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 5, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Aug 23, 2023Group: 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_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
Remark 999SEQUENCE THE SEQUENCES OF THE FAB COMPLEXES ARE NOT YET AVAILABLE IN ANY REFERENCE SEQUENCE ...SEQUENCE THE SEQUENCES OF THE FAB COMPLEXES ARE NOT YET AVAILABLE IN ANY REFERENCE SEQUENCE DATABASES. RESIDUE 50 IN CHAINS H,B,D and F WAS MUTATED FROM GLU TO ASP.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: Catalytic antibody 34E4 light chain
H: Catalytic antibody 34E4 heavy chain
A: Catalytic antibody 34E4 light chain
B: Catalytic antibody 34E4 heavy chain
C: Catalytic antibody 34E4 light chain
D: Catalytic antibody 34E4 heavy chain
E: Catalytic antibody 34E4 light chain
F: Catalytic antibody 34E4 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)192,40713
Polymers191,3268
Non-polymers1,0815
Water5,170287
1
L: Catalytic antibody 34E4 light chain
H: Catalytic antibody 34E4 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0933
Polymers47,8322
Non-polymers2611
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4310 Å2
ΔGint-31 kcal/mol
Surface area20040 Å2
MethodPISA
2
A: Catalytic antibody 34E4 light chain
B: Catalytic antibody 34E4 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0933
Polymers47,8322
Non-polymers2611
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4450 Å2
ΔGint-29 kcal/mol
Surface area19930 Å2
MethodPISA
3
C: Catalytic antibody 34E4 light chain
D: Catalytic antibody 34E4 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0933
Polymers47,8322
Non-polymers2611
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4550 Å2
ΔGint-29 kcal/mol
Surface area19730 Å2
MethodPISA
4
E: Catalytic antibody 34E4 light chain
F: Catalytic antibody 34E4 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1284
Polymers47,8322
Non-polymers2972
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4440 Å2
ΔGint-35 kcal/mol
Surface area19920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)163.000, 163.000, 151.200
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Antibody
Catalytic antibody 34E4 light chain


Mass: 23258.826 Da / Num. of mol.: 4 / Mutation: E(H50)D
Source method: isolated from a genetically manipulated source
Details: The variable domain (residues 1-107) is from a murine source and the constant domain (108-214) is from a human source
Source: (gene. exp.) Mus musculus, Homo sapiens / Genus: Mus, Homo / Species: , / Strain: , / Plasmid: p4xH-M13 / Production host: Escherichia coli (E. coli) / Strain (production host): TOPP2
#2: Antibody
Catalytic antibody 34E4 heavy chain


Mass: 24572.699 Da / Num. of mol.: 4 / Mutation: E(H50)D
Source method: isolated from a genetically manipulated source
Details: The variable domain (residues 1-113) is from a murine source and the constant domain (108-233) is from a human source
Source: (gene. exp.) Mus musculus, Homo sapiens / Genus: Mus, Homo / Species: , / Strain: , / Plasmid: p4xH-M13 / Production host: Escherichia coli (E. coli) / Strain (production host): TOPP2
#3: Chemical
ChemComp-HAN / 2-AMINO-5,6-DIMETHYL-BENZIMIDAZOLE-1-PENTANOIC ACID


Mass: 261.320 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H19N3O2
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 287 / 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: 3 Å3/Da / Density % sol: 57 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 8
Details: Diammonium hydrogen phosphate, NaCl, imidazole HCl, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 110K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 10, 2003
RadiationMonochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11587 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 57674 / Num. obs: 56867 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Biso Wilson estimate: 33.1 Å2 / Rsym value: 0.089 / Net I/σ(I): 8.2
Reflection shellResolution: 2.8→2.85 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 1.5 / Num. unique all: 2795 / Rsym value: 0.359 / % possible all: 98.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
CNS1.1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1Y0L

1y0l


Resolution: 2.8→50 Å / Isotropic thermal model: ANISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.252 2604 -RANDOM
Rwork0.215 ---
all0.217 57674 --
obs0.215 51110 5 %-
Displacement parametersBiso mean: 32 Å2
Baniso -1Baniso -2Baniso -3
1-3.96 Å23.96 Å2-7.92 Å2
2--8.84 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.51 Å0.46 Å
Refinement stepCycle: LAST / Resolution: 2.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13460 0 77 287 13824
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.017
RfactorNum. reflection% reflection
Rfree0.319 338 -
Rwork0.304 --
obs-7112 0.751 %

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