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- PDB-1riu: Anti-Cocaine Antibody M82G2 Complexed With Norbenzoylecgonine -

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Basic information

Entry
Database: PDB / ID: 1riu
TitleAnti-Cocaine Antibody M82G2 Complexed With Norbenzoylecgonine
Components
  • Fab M82G2, Heavy Chain
  • Fab M82G2, Light Chain
KeywordsIMMUNE SYSTEM / ANTI-COCAINE ANTIBODY / FAB
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Chem-RBE
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsPozharski, E. / Hewagama, A. / Shanafelt, A. / Petsko, G. / Ringe, D.
CitationJournal: To be Published
Title: Carving a Binding Site: Structural Study of an Anti-Cocaine Antibody in Complex with Three Cocaine Analogs
Authors: Pozharski, E. / Hewagama, A. / Shanafelt, A. / Petsko, G. / Ringe, D.
History
DepositionNov 18, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 2, 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 ...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 1.4Oct 30, 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)47,6793
Polymers47,4042
Non-polymers2751
Water3,495194
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3940 Å2
ΔGint-23 kcal/mol
Surface area19370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.700, 75.700, 153.21
Angle α, β, γ (deg.)90, 90, 120
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11L-222-

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: Chemical ChemComp-RBE / 3-(BENZOYLOXY)-8-AZA-BICYCLO[3.2.1]OCTANE-2-CARBOXYLIC ACID / NOR-BENZOYLECGONINE


Mass: 275.300 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H17NO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / 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: 2.55 Å3/Da / Density % sol: 51.3 %
Description: CRYSTALS WERE TRANSFERRED STEPWISE INTO 70% SATURATED SODIUM MALONATE, PH 7.2, AND SUBSEQUENTLY SOAKED OVERNIGHT IN THE SODIUM MALONATE SOLUTION CONTAINING 300 MICROMOLAR NORBENZOYLECGONINE-HCL
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 298K

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 7, 2002 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. all: 35109 / Num. obs: 35109 / % possible obs: 99.96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.3 % / Biso Wilson estimate: 38.4 Å2 / Rsym value: 0.12 / Net I/σ(I): 19
Reflection shellResolution: 2→2.07 Å / Redundancy: 8.3 % / Mean I/σ(I) obs: 1.75 / Num. unique all: 3437 / % possible all: 98.6

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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: 2→40 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: BULK SOLVENT MASK CORRECTED TO EXCLUDE INTERNAL CAVITIES
RfactorNum. reflection% reflectionSelection details
Rfree0.208 1740 5 %random
Rwork0.183 ---
all0.184 35109 --
obs0.184 35109 99.96 %-
Displacement parametersBiso mean: 29.9 Å2
Baniso -1Baniso -2Baniso -3
1--0.511 Å2-0.972 Å20 Å2
2---0.511 Å20 Å2
3---1.022 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.31 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 2→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3339 0 20 194 3553
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it2.121.5
X-RAY DIFFRACTIONc_mcangle_it3.042
X-RAY DIFFRACTIONc_scbond_it3.362
X-RAY DIFFRACTIONc_scangle_it4.622.5
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.58
X-RAY DIFFRACTIONc_dihedral_angle_d27.4
X-RAY DIFFRACTIONc_improper_angle_d0.95
LS refinement shellResolution: 2→2.07 Å
RfactorNum. reflection% reflection
Rfree0.325 156 4.6 %
Rwork0.388 3430 -
obs-3430 98.6 %

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