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Basic information

Entry
Database: PDB / ID: 4las
TitleCrystal structure of a therapeutic single chain antibody in complex with 4-hydroxymethamphetamine
ComponentsSingle chain antibody fragment scFv6H4
KeywordsIMMUNE SYSTEM / methamphetamine / anti-methamphetamine antibody / therapeutic antibody / scFv
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / 4-[(2S)-2-(methylamino)propyl]phenol
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 Å
AuthorsCelical, R. / Gokulan, K. / Peterson, E.C. / Varughese, K.I.
CitationJournal: Plos One / Year: 2013
Title: Structural characterization of a therapeutic anti-methamphetamine antibody fragment: oligomerization and binding of active metabolites.
Authors: Peterson, E.C. / Celikel, R. / Gokulan, K. / Varughese, K.I.
History
DepositionJun 20, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 2.0Dec 25, 2019Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / citation ...atom_site / citation / citation_author / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_symm_contact / pdbx_validate_torsion / struct / struct_asym / struct_conf / struct_conn / struct_mon_prot_cis / struct_ref / struct_ref_seq / struct_sheet_range / struct_site_gen
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _pdbx_entity_nonpoly.entity_id / _pdbx_nonpoly_scheme.asym_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.entity_id / _pdbx_nonpoly_scheme.ndb_seq_num / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_nonpoly_scheme.pdb_strand_id / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value / _pdbx_struct_sheet_hbond.range_1_auth_asym_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_asym_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_asym_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_asym_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _pdbx_validate_rmsd_angle.PDB_ins_code_3 / _pdbx_validate_rmsd_angle.auth_asym_id_1 / _pdbx_validate_rmsd_angle.auth_asym_id_2 / _pdbx_validate_rmsd_angle.auth_asym_id_3 / _pdbx_validate_rmsd_angle.auth_seq_id_1 / _pdbx_validate_rmsd_angle.auth_seq_id_2 / _pdbx_validate_rmsd_angle.auth_seq_id_3 / _pdbx_validate_rmsd_bond.auth_seq_id_1 / _pdbx_validate_rmsd_bond.auth_seq_id_2 / _pdbx_validate_torsion.auth_asym_id / _pdbx_validate_torsion.auth_seq_id / _struct.pdbx_descriptor / _struct.title / _struct_conf.beg_auth_asym_id / _struct_conf.beg_auth_seq_id / _struct_conf.beg_label_asym_id / _struct_conf.beg_label_seq_id / _struct_conf.end_auth_asym_id / _struct_conf.end_auth_seq_id / _struct_conf.end_label_asym_id / _struct_conf.end_label_seq_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_seq_id / _struct_mon_prot_cis.auth_asym_id / _struct_mon_prot_cis.auth_seq_id / _struct_mon_prot_cis.label_asym_id / _struct_mon_prot_cis.label_seq_id / _struct_mon_prot_cis.pdbx_auth_asym_id_2 / _struct_mon_prot_cis.pdbx_auth_seq_id_2 / _struct_mon_prot_cis.pdbx_label_asym_id_2 / _struct_mon_prot_cis.pdbx_label_seq_id_2 / _struct_sheet_range.beg_auth_asym_id / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.beg_label_asym_id / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_auth_asym_id / _struct_sheet_range.end_auth_seq_id / _struct_sheet_range.end_label_asym_id / _struct_sheet_range.end_label_seq_id / _struct_site_gen.auth_asym_id / _struct_site_gen.auth_seq_id / _struct_site_gen.label_asym_id / _struct_site_gen.label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Single chain antibody fragment scFv6H4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,9582
Polymers26,7921
Non-polymers1651
Water1,27971
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.279, 65.297, 48.574
Angle α, β, γ (deg.)90.00, 98.36, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody Single chain antibody fragment scFv6H4


Mass: 26792.344 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: PPICZ-ALPHA / Production host: Komagataella pastoris (fungus) / Strain (production host): KM71H
#2: Chemical ChemComp-1WF / 4-[(2S)-2-(methylamino)propyl]phenol / 4-Hydroxymethamphetamine / Pholedrine


Mass: 165.232 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15NO
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 71 / Source method: isolated from a natural source / Formula: H2O

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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: 2.13 Å3/Da / Density % sol: 42.25 %
Crystal growTemperature: 287.15 K / pH: 8
Details: 1.6M ammonium sulfate, 240 mM imidazole malate, pH 8.0., VAPOR DIFFUSION, HANGING DROP, temperature 287.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 17, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.33→50 Å / Num. obs: 8577 / % possible obs: 93.3 % / Redundancy: 3 % / Rmerge(I) obs: 0.053 / Rsym value: 0.03 / Net I/σ(I): 32.4

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
CNSrefinement
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.33→33.94 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.921 / SU B: 7.494 / SU ML: 0.181 / Cross valid method: THROUGHOUT / ESU R: 0.636 / ESU R Free: 0.275 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.238 405 4.7 %RANDOM
Rwork0.16 ---
obs0.164 8164 93.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.22 Å2
Baniso -1Baniso -2Baniso -3
1-2.09 Å2-0 Å20.36 Å2
2---1.16 Å2-0 Å2
3----0.95 Å2
Refinement stepCycle: LAST / Resolution: 2.33→33.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1777 0 12 71 1860
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.021825
X-RAY DIFFRACTIONr_bond_other_d0.0010.021621
X-RAY DIFFRACTIONr_angle_refined_deg1.5941.9542460
X-RAY DIFFRACTIONr_angle_other_deg0.83.0023742
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1555218
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.39323.71470
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.74815285
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.213156
X-RAY DIFFRACTIONr_chiral_restr0.0920.2268
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212002
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02416
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.33→2.39 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.258 42 -
Rwork0.171 574 -
obs--92.77 %

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