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- PDB-1rfd: ANTI-COCAINE ANTIBODY M82G2 -

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Basic information

Entry
Database: PDB / ID: 1rfd
TitleANTI-COCAINE ANTIBODY M82G2
Components
  • Fab M82G2, Heavy Chain
  • Fab M82G2, Light Chain
KeywordsIMMUNE SYSTEM / ANTI-COCAINE ANTIBODY / FAB
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsPozharski, E. / 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
DepositionNov 7, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 999SEQUENCE NO DATABASE REFERENCE SEQUENCE WAS FOUND FOR EITHER PROTEIN IN THIS STRUCTURE AT THE TIME ...SEQUENCE NO DATABASE REFERENCE SEQUENCE WAS FOUND FOR EITHER PROTEIN IN THIS STRUCTURE AT THE TIME OF PROCESSING.

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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


Theoretical massNumber of molelcules
Total (without water)47,4042
Polymers47,4042
Non-polymers00
Water4,270237
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3250 Å2
ΔGint-23 kcal/mol
Surface area19310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.916, 74.916, 151.268
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-223-

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: 23519.264 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 237 / 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: 2.58 Å3/Da / Density % sol: 52.39 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: 2M AMMONIUM SULFATE, 5% ISO-PROPANOL, pH 5.20, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 30, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.09→30 Å / Num. all: 26932 / Num. obs: 26932 / % possible obs: 90.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Biso Wilson estimate: 38.5 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 25.4
Reflection shellResolution: 2.09→2.16 Å / Redundancy: 5.8 % / Mean I/σ(I) obs: 4.8 / Num. unique all: 2603 / % possible all: 88.9

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QYG

1qyg


Resolution: 2.09→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
Rfree0.226 1311 4 %random
Rwork0.183 ---
all0.185 26932 --
obs0.185 26932 90.2 %-
Displacement parametersBiso mean: 0.303 Å2
Baniso -1Baniso -2Baniso -3
1-0.313 Å20.856 Å20 Å2
2--0.313 Å20 Å2
3----0.625 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 2.09→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3339 0 0 237 3576
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.71
X-RAY DIFFRACTIONc_dihedral_angle_d27.6
X-RAY DIFFRACTIONc_improper_angle_d0.955
X-RAY DIFFRACTIONc_mcbond_it2.111.5
X-RAY DIFFRACTIONc_mcangle_it3.052
X-RAY DIFFRACTIONc_scbond_it3.172
X-RAY DIFFRACTIONc_scangle_it4.242.5
LS refinement shellResolution: 2.09→2.16 Å
RfactorNum. reflection% reflection
Rfree0.265 125 4.2 %
Rwork0.211 2535 -
obs-2494 84.7 %

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