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

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Basic information

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


IgG immunoglobulin complex / 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 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
COCAINE / Vh gene product / Immunoglobulin kappa constant / :
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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 1.3Aug 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 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'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2293
Polymers47,9252
Non-polymers3031
Water7,927440
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4420 Å2
ΔGint-20 kcal/mol
Surface area19450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.254, 117.320, 85.217
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11H-468-

HOH

21H-470-

HOH

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Components

#1: Antibody Antibody 7A1 Fab'


Mass: 24059.611 Da / Num. of mol.: 1 / Fragment: IMMUNOGLOBULIN IGG1 KAPPA LIGHT CHAIN / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Strain: Mouse / References: UniProt: Q5XKG4, UniProt: P01837*PLUS
#2: Antibody Antibody 7A1 Fab'


Mass: 23865.783 Da / Num. of mol.: 1 / Fragment: IMMUNOGLOBULIN IGG1 HEAVY CHAIN / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Strain: Mouse / References: UniProt: A2NUE8
#3: Chemical ChemComp-COC / COCAINE / Cocaine


Mass: 303.353 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21NO4 / Comment: alkaloid*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 440 / 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: 2.3 Å3/Da / Density % sol: 46.5 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: PEG 4000, ammonium formate, 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: 8.2.1 / Wavelength: 1.0688 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 11, 2003
RadiationMonochromator: Double Crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0688 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 72094 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.052
Reflection shellResolution: 1.5→1.54 Å / Rmerge(I) obs: 0.66 / % possible all: 97.7

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Processing

SoftwareName: REFMAC / Version: 5.1.9999 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2AJS

2ajs


Resolution: 1.5→48.22 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.956 / SU B: 3.515 / SU ML: 0.058 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.094 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22684 3661 5.1 %RANDOM
Rwork0.18183 ---
obs0.18407 68409 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 28.332 Å2
Baniso -1Baniso -2Baniso -3
1--0.91 Å20 Å20 Å2
2---0.3 Å20 Å2
3---1.21 Å2
Refinement stepCycle: LAST / Resolution: 1.5→48.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3416 0 22 440 3878
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223536
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5711.9444833
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.885428
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.82523.813139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.03815571
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9141517
X-RAY DIFFRACTIONr_chiral_restr0.1120.2560
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022609
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2140.21628
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.2392
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.170.244
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1950.221
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5931.52233
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.45223593
X-RAY DIFFRACTIONr_scbond_it3.08731499
X-RAY DIFFRACTIONr_scangle_it4.3634.51228
X-RAY DIFFRACTIONr_rigid_bond_restr1.91333732
X-RAY DIFFRACTIONr_sphericity_free6.0853442
X-RAY DIFFRACTIONr_sphericity_bonded4.32133438
LS refinement shellHighest resolution: 1.5 Å / Num. reflection Rwork: 4897 / Total num. of bins used: 20

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