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- PDB-3gm0: Anti-methamphetamine single chain Fv in complex with MDMA -

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Basic information

Entry
Database: PDB / ID: 3gm0
TitleAnti-methamphetamine single chain Fv in complex with MDMA
Componentsanti-methamphetamine single chain Fv
KeywordsIMMUNE SYSTEM / anti-methamphetamine antibody / single chain Fv / Therapeutic antibody
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Chem-B41
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 Å
AuthorsCelikel, R. / Peterson, E.C. / Owens, M. / Varughese, K.I.
CitationJournal: Protein Sci. / Year: 2009
Title: Crystal structures of a therapeutic single chain antibody in complex with two drugs of abuse-Methamphetamine and 3,4-methylenedioxymethamphetamine.
Authors: Celikel, R. / Peterson, E.C. / Owens, S.M. / Varughese, K.I.
History
DepositionMar 12, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 6, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: anti-methamphetamine single chain Fv
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9832
Polymers27,7891
Non-polymers1931
Water1,38777
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.720, 64.806, 48.322
Angle α, β, γ (deg.)90.000, 98.970, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody anti-methamphetamine single chain Fv


Mass: 27789.309 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: IgG / Plasmid: pPICZ-alpha / Production host: Pichia pastoris (fungus) / Strain (production host): KM71H
#2: Chemical ChemComp-B41 / (2S)-1-(1,3-benzodioxol-5-yl)-N-methylpropan-2-amine / 3,4 methylenedioxy-n-methylamphetamine, MDMA, Ecstasy / MDMA


Mass: 193.242 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H15NO2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE PROTEIN WAS CRYSTALLIZED AS A FUSION PROTEIN WHERE TWO CHAINS, CHAIN H AND CHAIN L, WERE FUSED ...THE PROTEIN WAS CRYSTALLIZED AS A FUSION PROTEIN WHERE TWO CHAINS, CHAIN H AND CHAIN L, WERE FUSED TOGETHER INTO ONE CHAIN USING A 15-RESIDUE LINKER. THE SEQUENCE OF THE LINKER IS: GGGGS GGGGS GGGGS. IN ADDITION, THERE IS A FLAG EPITOPE AT THE N-TERMINAL AND THERE IS A HIS-TAG AT THE C-TERMINAL. PLEASE NOTE THAT THE AMINO ACID NUMBERING IN THIS PDB FILE A SEQUENTIAL NUMBERING OF THE SCFV6H4 SINGLE CHAIN ANTIBODY AMINO ACIDS DUE TO PDB POLICY. PLEASE SEE THE ORIGINAL MANUSCRIPT FOR THE MORE COMMON KABAT AMINO ACID NUMBERING SCHEME OF THE HEAVY AND LIGHT CHAIN RESIDUES. PLEASE USE THE CORRELATION PROVIDED BELOW FOR CONVERTING TO KABAT NUMBERING SCHEME USED IN OUR MANUSCRIPT. PDB NUMBER (PUBLICATION NUMBER): A9 (H1), A90 (H82), A91 (H82A), A92 (H82B), A93 (H82C), A94 (H93), A110 (H99), A111 (H100A), A112 (H100B), A113 (H100C), A114 (H101), A141 (L1), A167 (L27), A168 (L27A), A169 (L28), A247 (L106), A248 (L106A), A249 (L107), HOH 505 (OW(5)), HOH 506 (OW(6))

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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: 1.93 Å3/Da / Density % sol: 36.35 %
Crystal growTemperature: 287 K / Method: vapor diffusion / pH: 8.3
Details: 1.15M sodium Citrate, 0.28M Imidazole malate, pH 8.3, VAPOR DIFFUSION, temperature 287K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.97945 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 18, 2008 / Details: single crystal bent monochromator
RadiationMonochromator: single crystal bent monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 2.4→32.4 Å / Num. all: 8316 / Num. obs: 8316 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Redundancy: 3.75 % / Rsym value: 0.045
Reflection shellResolution: 2.4→2.58 Å / Redundancy: 3.7 % / Rsym value: 0.21 / % possible all: 99.5

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT3.006data extraction
ADSCQuantumdata collection
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementResolution: 2.4→15 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.271 592 7.1 %
Rwork0.214 --
obs-8316 99.8 %
Solvent computationBsol: 66.944 Å2
Displacement parametersBiso max: 82.68 Å2 / Biso mean: 39.042 Å2 / Biso min: 16.72 Å2
Baniso -1Baniso -2Baniso -3
1-16.17 Å20 Å21.382 Å2
2---11.194 Å20 Å2
3----4.976 Å2
Refine analyzeLuzzati coordinate error obs: 0.32 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.32 Å
Refinement stepCycle: LAST / Resolution: 2.4→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1797 0 14 77 1888
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_d1.337
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDNum. reflection obs
2.4-2.670.3451630.311X-RAY DIFFRACTION2092
2.67-2.930.3121030.251X-RAY DIFFRACTION1505
2.93-3.350.3141150.219X-RAY DIFFRACTION1512
3.35-4.210.2621040.195X-RAY DIFFRACTION1501
4.21-150.2191050.186X-RAY DIFFRACTION1541
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water.param
X-RAY DIFFRACTION3mdma.param

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