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- PDB-3gkz: Crystal structures of a therapeutic single chain antibody in comp... -

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Basic information

Entry
Database: PDB / ID: 3gkz
TitleCrystal structures of a therapeutic single chain antibody in complex methamphetamine
Componentsanti-methamphetamine single chain Fv
KeywordsIMMUNE SYSTEM / Therapeutic antibody / Methamphetamine / amphetamine / MDMA / IgG
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / (2S)-N-methyl-1-phenylpropan-2-amine
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 11, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 6, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 11, 2019Group: Data collection / Refinement description / Category: refine_ls_shell
Item: _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)27,9392
Polymers27,7891
Non-polymers1491
Water1,72996
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.338, 65.265, 48.513
Angle α, β, γ (deg.)90.00, 98.75, 90.00
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-B40 / (2S)-N-methyl-1-phenylpropan-2-amine / Methamphetamine


Mass: 149.233 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
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: 36.38 %
Crystal growTemperature: 287 K / Method: vapor diffusion / pH: 8
Details: 1.15M sidium citrate, 0.28M imidazole malate, pH 8.0, VAPOR DIFFUSION, temperature 287K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.97946 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 17, 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: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.9→38.64 Å / Num. all: 16710 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Redundancy: 6.7 % / Rsym value: 0.05 / Net I/σ(I): 33.2
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 4.9 / Num. unique all: 1470 / Rsym value: 0.188 / % possible all: 89.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→38.64 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 84552.39 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.235 1142 6.9 %RANDOM
Rwork0.21 ---
obs0.21 16519 98.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 47.5645 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 23.8 Å2
Baniso -1Baniso -2Baniso -3
1-6.44 Å20 Å21.82 Å2
2---5.05 Å20 Å2
3----1.39 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 1.9→38.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1781 0 11 96 1888
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d26.7
X-RAY DIFFRACTIONc_improper_angle_d0.71
X-RAY DIFFRACTIONc_mcbond_it1.371.5
X-RAY DIFFRACTIONc_mcangle_it2.052
X-RAY DIFFRACTIONc_scbond_it2.222
X-RAY DIFFRACTIONc_scangle_it2.992.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection obs% reflection obs (%)
1.9-2.030.2681786.90.24223860.02309292.7
2.03-2.160.281510.2152216
2.16-2.320.2451480.2092285
2.32-2.660.2562180.233034
2.66-3.340.2692020.2223010
3.34-150.19352210.1913095
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water.param
X-RAY DIFFRACTION3meth.param

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