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- PDB-2ak1: Crystal Structure of Cocaine catalytic Antibody 7A1 Fab' in Compl... -

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Basic information

Entry
Database: PDB / ID: 2ak1
TitleCrystal Structure of Cocaine catalytic Antibody 7A1 Fab' in Complex with benzoic acid
Components(Antibody 7A1 Fab') x 2
KeywordsIMMUNE SYSTEM / catalytic Antibody / Fab / benzoic acid / HYDROLYTIC
Function / homology
Function and homology information


B cell differentiation / 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 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
BENZOIC ACID / Immunoglobulin kappa constant / IgG-2a protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 16, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)48,3097
Polymers47,9252
Non-polymers3845
Water5,981332
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4420 Å2
ΔGint-127 kcal/mol
Surface area19630 Å2
MethodPISA
2
L: Antibody 7A1 Fab'
hetero molecules

L: Antibody 7A1 Fab'
hetero molecules

H: Antibody 7A1 Fab'
hetero molecules

H: Antibody 7A1 Fab'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,61814
Polymers95,8514
Non-polymers76810
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
crystal symmetry operation5_555x+1/2,y+1/2,z1
crystal symmetry operation8_556x+1/2,-y+1/2,-z+11
Buried area2670 Å2
ΔGint-241 kcal/mol
Surface area45410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.595, 89.106, 153.454
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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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) / References: 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) / References: UniProt: Q5M842*PLUS
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-BEZ / BENZOIC ACID


Mass: 122.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 332 / 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: 2.9 Å3/Da / Density % sol: 57.6 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: PEG 4000, zinc acetate, 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: 8.2.2 / Wavelength: 1.0781 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 22, 2003
RadiationMonochromator: DOUBLE-CRYSTAL, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0781 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 48913 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.058 / Χ2: 1.541
Reflection shellResolution: 1.85→1.89 Å / % possible obs: 97.9 % / Rmerge(I) obs: 0.571 / Num. measured obs: 3166 / Χ2: 0.628 / % possible all: 97.9

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Processing

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

2ajs


Resolution: 1.85→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.238 2334 4.8 %RANDOM
Rwork0.217 ---
obs-46346 95.3 %-
Solvent computationBsol: 43.458 Å2
Displacement parametersBiso mean: 41.095 Å2
Baniso -1Baniso -2Baniso -3
1--9.999 Å20 Å20 Å2
2--9.217 Å20 Å2
3---0.782 Å2
Refinement stepCycle: LAST / Resolution: 1.85→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3373 0 13 332 3718
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4

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