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- PDB-1q72: Anti-Cocaine Antibody M82G2 Complexed with Cocaine -

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Basic information

Entry
Database: PDB / ID: 1q72
TitleAnti-Cocaine Antibody M82G2 Complexed with Cocaine
Components
  • Fab M82G2, Heavy chain
  • Fab M82G2, Light chain
KeywordsIMMUNE SYSTEM / ANTI-COCAINE ANTIBODY / FAB
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / COCAINE
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsPozharski, E. / Moulin, A. / Hewagama, A. / Shanafelt, A.B. / Petsko, G.A. / Ringe, D.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Diversity in hapten recognition: structural study of an anti-cocaine antibody M82G2.
Authors: Pozharski, E. / Moulin, A. / Hewagama, A. / Shanafelt, A.B. / Petsko, G.A. / Ringe, D.
History
DepositionAug 15, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: Fab M82G2, Light chain
H: Fab M82G2, Heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6633
Polymers47,3602
Non-polymers3031
Water6,017334
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3840 Å2
ΔGint-22 kcal/mol
Surface area19270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.386, 75.386, 150.817
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11L-314-

HOH

21H-518-

HOH

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Components

#1: Antibody Fab M82G2, Light chain


Mass: 23884.365 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#2: Antibody Fab M82G2, Heavy chain


Mass: 23475.209 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Chemical ChemComp-COC / COCAINE


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


Mass: 18.015 Da / Num. of mol.: 334 / 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: 2.61 Å3/Da / Density % sol: 52.91 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: 2M ammonium sulfate, 5% iso-propanol, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mMTris-HCl1droppH8.0
25 mg/mlprotein1drop
32 Mammonium sulfate1reservoir
45 %(v/v)isopropanol1reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 27, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. all: 54352 / Num. obs: 54352 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Biso Wilson estimate: 34.1 Å2 / Rmerge(I) obs: 0.125 / Net I/σ(I): 13.1
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 2 / Num. unique all: 5220 / % possible all: 97.9
Reflection
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 30 Å / Num. measured all: 348644
Reflection shell
*PLUS
% possible obs: 97.9 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AR3 (CONSTANT DOMAIN) + PDB ENTRY 1AXT (VARIABLE DOMAIN)

1ar3
PDB Unreleased entry

1axt


Resolution: 1.7→30 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: BULK SOLVENT MASK CORRECTED TO EXCLUDE INTERNAL CAVITIES
RfactorNum. reflection% reflectionSelection details
Rfree0.249 2754 -RANDOM
Rwork0.218 ---
all0.22 54347 --
obs0.22 54347 98.1 %-
Displacement parametersBiso mean: 30.1 Å2
Baniso -1Baniso -2Baniso -3
1-3.569 Å22.212 Å20 Å2
2--3.751 Å20 Å2
3----7.32 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 1.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3454 0 22 334 3810
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.397
X-RAY DIFFRACTIONc_dihedral_angle_deg26.8
X-RAY DIFFRACTIONc_improper_angle_deg0.82
LS refinement shellResolution: 1.7→1.76 Å
RfactorNum. reflection% reflection
Rfree0.354 288 -
Rwork0.297 --
obs-5331 97.6 %
Refinement
*PLUS
Num. reflection Rfree: 1277
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_improper_angle_deg0.82

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