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- PDB-2ajz: Crystal Structure of Cocaine catalytic Antibody 7A1 Fab' in Compl... -

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Basic information

Entry
Database: PDB / ID: 2ajz
TitleCrystal Structure of Cocaine catalytic Antibody 7A1 Fab' in Complex with ecgonine methyl ester
Components(Antibody 7A1 Fab') x 2
KeywordsIMMUNE SYSTEM / catalytic Antibody / Fab / ecgonine methyl ester / HYDROLYTIC
Function / homology
Function and homology information


immunoglobulin complex / B cell differentiation / adaptive immune response / extracellular region / 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
Chem-ECG / Vh gene product / Immunoglobulin kappa constant
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsZhu, X. / Wilson, I.A.
CitationJournal: Structure / Year: 2006
Title: Complete reaction cycle of a cocaine catalytic antibody at atomic resolution.
Authors: Zhu, X. / Dickerson, T.J. / Rogers, C.J. / Kaufmann, G.F. / Mee, J.M. / McKenzie, K.M. / Janda, K.D. / Wilson, I.A.
History
DepositionAug 2, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 14, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
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
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 999SEQUENCE The sequence of these proteins are not available at any sequence database at the time of processing.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: Antibody 7A1 Fab'
H: Antibody 7A1 Fab'
A: Antibody 7A1 Fab'
B: Antibody 7A1 Fab'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,2496
Polymers95,8514
Non-polymers3982
Water4,738263
1
L: Antibody 7A1 Fab'
H: Antibody 7A1 Fab'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1253
Polymers47,9252
Non-polymers1991
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4100 Å2
ΔGint-21 kcal/mol
Surface area19850 Å2
MethodPISA
2
A: Antibody 7A1 Fab'
B: Antibody 7A1 Fab'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1253
Polymers47,9252
Non-polymers1991
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4080 Å2
ΔGint-22 kcal/mol
Surface area20030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.934, 78.489, 130.334
Angle α, β, γ (deg.)90.00, 91.87, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody Antibody 7A1 Fab'


Mass: 24059.611 Da / Num. of mol.: 2 / Fragment: IMMUNOGLOBULIN IGG1 KAPPA LIGHT CHAIN / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P01837*PLUS
#2: Antibody Antibody 7A1 Fab'


Mass: 23865.783 Da / Num. of mol.: 2 / Fragment: IMMUNOGLOBULIN IGG1 heavy CHAIN / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: A2NUE8
#3: Chemical ChemComp-ECG / 3-HYDROXY-8-METHYL-8-AZA-BICYCLO[3.2.1]OCTANE-2-CARBOXYLIC ACID METHYL ESTER / ECGONINE METHYL ESTER


Mass: 199.247 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17NO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 263 / 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: 2.6 Å3/Da / Density % sol: 52.7 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: PEG 4000, ammonium fluoride, sodium acetate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Aug 8, 2003
RadiationMonochromator: DOUBLE-CRYSTAL, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 40412 / % possible obs: 90.2 % / Rmerge(I) obs: 0.099 / Χ2: 3.303
Reflection shellResolution: 2.3→2.38 Å / % possible obs: 65.2 % / Rmerge(I) obs: 0.363 / Num. measured obs: 2905 / Χ2: 3.576 / % possible all: 65.2

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT1.7data extraction
HKL-2000data reduction
HKL-2000data scaling
COMOphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDb ENTRY 2AJS

2ajs


Resolution: 2.3→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.285 1878 4.4 %RANDOM
Rwork0.238 ---
obs-37144 86.2 %-
Solvent computationBsol: 60.308 Å2
Displacement parametersBiso mean: 35.657 Å2
Baniso -1Baniso -2Baniso -3
1-6.395 Å20 Å2-5.054 Å2
2--6.203 Å20 Å2
3----12.598 Å2
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6746 0 28 263 7037
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.6

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