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- PDB-8y57: Anti MDMA antibody 1bB11 complex -

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Basic information

Entry
Database: PDB / ID: 8y57
TitleAnti MDMA antibody 1bB11 complex
Components
  • Heavy chain of 1bB11
  • Light chain of 1bB11
KeywordsIMMUNE SYSTEM / Antibody / Ecstasy
Function / homologyChem-B41
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsCheon, G. / Lee, Y. / Lee, S.
Funding support Korea, Republic Of, 5items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2017R1A5A1014560 Korea, Republic Of
National Research Foundation (NRF, Korea)RS-2023-00223552 Korea, Republic Of
National Research Foundation (NRF, Korea)2021M3A9I4022936 Korea, Republic Of
National Research Foundation (NRF, Korea)2020M3A9E4038938 Korea, Republic Of
National Research Foundation (NRF, Korea)2022R1A2C100988211 Korea, Republic Of
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2024
Title: Crystal structure of an antibody specifically recognizing 3,4-methyl enedioxy methamphetamine through the epoxide moiety.
Authors: Cheon, G. / Hwang, D. / Le, T.C. / Lee, Y. / Han, E. / An, S. / Jung, Y. / Chung, H. / Lee, S.
History
DepositionJan 31, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 11, 2024Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2024Group: Database references / Category: citation
Item: _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Heavy chain of 1bB11
D: Light chain of 1bB11
A: Heavy chain of 1bB11
B: Light chain of 1bB11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,5975
Polymers97,4044
Non-polymers1931
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)254.120, 254.120, 254.120
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number214
Space group name H-MI4132
Space group name HallI4bd2c3
Symmetry operation#1: x,y,z
#2: x+1/4,-z+1/4,y+3/4
#3: x+1/4,z+3/4,-y+3/4
#4: z+1/4,y+3/4,-x+3/4
#5: -z+1/4,y+3/4,x+1/4
#6: -y+1/4,x+3/4,z+1/4
#7: y+1/4,-x+1/4,z+3/4
#8: z,x,y
#9: y,z,x
#10: -y,-z+1/2,x
#11: z,-x,-y+1/2
#12: -y+1/2,z,-x
#13: -z,-x+1/2,y
#14: -z+1/2,x,-y
#15: y,-z,-x+1/2
#16: x,-y,-z+1/2
#17: -x+1/2,y,-z
#18: -x,-y+1/2,z
#19: y+1/4,x+3/4,-z+3/4
#20: -y+1/4,-x+1/4,-z+1/4
#21: z+1/4,-y+1/4,x+3/4
#22: -z+1/4,-y+1/4,-x+1/4
#23: -x+1/4,z+3/4,y+1/4
#24: -x+1/4,-z+1/4,-y+1/4
#25: x+1/2,y+1/2,z+1/2
#26: x+3/4,-z+3/4,y+5/4
#27: x+3/4,z+5/4,-y+5/4
#28: z+3/4,y+5/4,-x+5/4
#29: -z+3/4,y+5/4,x+3/4
#30: -y+3/4,x+5/4,z+3/4
#31: y+3/4,-x+3/4,z+5/4
#32: z+1/2,x+1/2,y+1/2
#33: y+1/2,z+1/2,x+1/2
#34: -y+1/2,-z+1,x+1/2
#35: z+1/2,-x+1/2,-y+1
#36: -y+1,z+1/2,-x+1/2
#37: -z+1/2,-x+1,y+1/2
#38: -z+1,x+1/2,-y+1/2
#39: y+1/2,-z+1/2,-x+1
#40: x+1/2,-y+1/2,-z+1
#41: -x+1,y+1/2,-z+1/2
#42: -x+1/2,-y+1,z+1/2
#43: y+3/4,x+5/4,-z+5/4
#44: -y+3/4,-x+3/4,-z+3/4
#45: z+3/4,-y+3/4,x+5/4
#46: -z+3/4,-y+3/4,-x+3/4
#47: -x+3/4,z+5/4,y+3/4
#48: -x+3/4,-z+3/4,-y+3/4

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Components

#1: Antibody Heavy chain of 1bB11


Mass: 24889.729 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Plasmid: pSF vector / Cell line (production host): Expi293F / Production host: Homo sapiens (human)
#2: Antibody Light chain of 1bB11


Mass: 23812.324 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Plasmid: pSF vector / Cell line (production host): Expi293F / Production host: Homo sapiens (human)
#3: Chemical ChemComp-B41 / (2S)-1-(1,3-benzodioxol-5-yl)-N-methylpropan-2-amine / 3,4 methylenedioxy-n-methylamphetamine / MDMA / Ecstasy


Mass: 193.242 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H15NO2 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
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: 3.35 Å3/Da / Density % sol: 63.3 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 44%(v/v) PEG-400, pH 7.0 imidazole, 0.2M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.9794 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 27, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 3.2→49.84 Å / Num. obs: 23445 / % possible obs: 99.7 % / Redundancy: 75.9 % / Biso Wilson estimate: 84.3 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.303 / Rpim(I) all: 0.035 / Rrim(I) all: 0.305 / Net I/σ(I): 16.3
Reflection shellResolution: 3.2→3.314 Å / Rmerge(I) obs: 0.303 / Mean I/σ(I) obs: 16.3 / Num. unique obs: 1142 / CC1/2: 0.989 / Rpim(I) all: 0.035 / Rrim(I) all: 0.305

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
HKL-2000v717data reduction
HKL-2000v717data scaling
PHENIX1.19_4092phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→49.84 Å / SU ML: 0.4896 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 31.1716
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3011 2000 8.54 %
Rwork0.2427 21420 -
obs0.2476 23420 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 83.41 Å2
Refinement stepCycle: LAST / Resolution: 3.2→49.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6411 0 14 0 6425
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00186570
X-RAY DIFFRACTIONf_angle_d0.46228931
X-RAY DIFFRACTIONf_chiral_restr0.04041005
X-RAY DIFFRACTIONf_plane_restr0.00431142
X-RAY DIFFRACTIONf_dihedral_angle_d16.65062336
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.280.38971390.34111497X-RAY DIFFRACTION99.88
3.28-3.360.35111410.31771499X-RAY DIFFRACTION100
3.37-3.460.3841410.29191509X-RAY DIFFRACTION100
3.46-3.570.32291390.27991496X-RAY DIFFRACTION100
3.58-3.70.32311410.29351513X-RAY DIFFRACTION100
3.7-3.850.35551410.27241508X-RAY DIFFRACTION100
3.85-4.030.32611410.25471509X-RAY DIFFRACTION100
4.03-4.240.3341420.24351528X-RAY DIFFRACTION100
4.24-4.50.27971420.21611513X-RAY DIFFRACTION100
4.5-4.850.261430.20171530X-RAY DIFFRACTION100
4.85-5.340.22941430.20611532X-RAY DIFFRACTION100
5.34-6.110.31611450.23511559X-RAY DIFFRACTION100
6.11-7.690.28931460.25051564X-RAY DIFFRACTION100
7.7-49.840.27961560.21831663X-RAY DIFFRACTION99.67

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