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- PDB-1ktr: Crystal Structure of the Anti-His Tag Antibody 3D5 Single-Chain F... -

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Entry
Database: PDB / ID: 1ktr
TitleCrystal Structure of the Anti-His Tag Antibody 3D5 Single-Chain Fragment (scFv) in Complex with a Oligohistidine peptide
Components
  • Anti-his tag antibody 3d5 variable light chain, Peptide linker, Anti-his tag antibody 3d5 variable heavy chain
  • Oligohistidine peptide Antigen
KeywordsIMMUNE SYSTEM / immunoglobulin domains / single chain antibody-antigen complex / His tag recognition / scfv
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsKaufmann, M. / Lindner, P. / Honegger, A. / Blank, K. / Tschopp, M. / Capitani, G. / Plueckthun, A. / Gruetter, M.G.
Citation
Journal: J.Mol.Biol. / Year: 2002
Title: Crystal structure of the anti-His tag antibody 3D5 single-chain fragment complexed to its antigen.
Authors: Kaufmann, M. / Lindner, P. / Honegger, A. / Blank, K. / Tschopp, M. / Capitani, G. / Pluckthun, A. / Grutter, M.G.
#1: Journal: BIO*TECHNIQUES / Year: 1997
Title: Specific detection of his-tagged proteins with recombinant anti-His tag scFv-phosphatase or scFv-phage fusions
Authors: Lindner, P. / Bauer, K. / Krebber, A. / Nieba, L. / Kremmer, E. / Krebber, C. / Honegger, A. / Klinger, B. / Mocikat, R. / Plueckthun, A.
History
DepositionJan 17, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0May 2, 2018Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / entity ...atom_site / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_entity_nonpoly / pdbx_entity_src_syn / pdbx_entry_details / 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_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_torsion / struct_asym / struct_conf / struct_conn / struct_mon_prot_cis / struct_ref / struct_ref_seq / struct_sheet_range
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _entity_poly_seq.entity_id / _entity_poly_seq.num / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_src_syn.entity_id / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific / _pdbx_entity_src_syn.pdbx_beg_seq_num / _pdbx_entity_src_syn.pdbx_end_seq_num / _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_poly_seq_scheme.asym_id / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.entity_id / _pdbx_poly_seq_scheme.ndb_seq_num / _pdbx_poly_seq_scheme.pdb_ins_code / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_poly_seq_scheme.pdb_seq_num / _pdbx_poly_seq_scheme.pdb_strand_id / _pdbx_poly_seq_scheme.seq_id / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _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_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.label_seq_id / _pdbx_unobs_or_zero_occ_residues.PDB_ins_code / _pdbx_unobs_or_zero_occ_residues.auth_asym_id / _pdbx_unobs_or_zero_occ_residues.auth_comp_id / _pdbx_unobs_or_zero_occ_residues.auth_seq_id / _pdbx_unobs_or_zero_occ_residues.label_asym_id / _pdbx_unobs_or_zero_occ_residues.label_comp_id / _pdbx_unobs_or_zero_occ_residues.label_seq_id / _pdbx_validate_torsion.auth_seq_id / _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_seq_id / _struct_mon_prot_cis.pdbx_auth_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
Revision 2.1Aug 16, 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_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Remark 999SEQUENCE Neither the sequence of the wild-type nor the mutated sequence, from which the structure ...SEQUENCE Neither the sequence of the wild-type nor the mutated sequence, from which the structure was solved, was deposited to a database. In comparison to the wild-type of the anti-his tag antibody 3d5 variable light chain, the mutated sequence chain L has the following mutations: L9S, V78F, Y88D. In comparison to the wild-type of the anti-his tag antibody 3d5 variable heavy chain, the mutated sequence chain H has the following mutations: L12D, H48P, S51G, K77R, E100D, L144T. The scfv, consisting of chains L, M, and H, was expressed as one polypeptide. The N-terminal variable light chain, chain L and the C-terminal variable heavy chain, chain H are connected by the peptide linker, chain M. Note that chains L, M, and H are one continuous polypeptide chain and most of the linker, chain M, is invisible. The first three residues of chain L, DYK, are part of the flag recognition tag.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: Anti-his tag antibody 3d5 variable light chain, Peptide linker, Anti-his tag antibody 3d5 variable heavy chain
P: Oligohistidine peptide Antigen


Theoretical massNumber of molelcules
Total (without water)27,3222
Polymers27,3222
Non-polymers00
Water2,810156
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area750 Å2
ΔGint-2 kcal/mol
Surface area10960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.51, 106.51, 92.80
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Antibody Anti-his tag antibody 3d5 variable light chain, Peptide linker, Anti-his tag antibody 3d5 variable heavy chain


Mass: 26475.104 Da / Num. of mol.: 1
Mutation: L9S, V78F, Y88D, L12D, H48P, S51G, K77R, E100D, L144T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Monoclonal Antibody 3D5 / Plasmid: pAK1Hmut1+2_noM / Production host: Escherichia coli (E. coli) / Strain (production host): SB536
#2: Protein/peptide Oligohistidine peptide Antigen


Mass: 846.896 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: The peptide was chemically synthetized. / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 156 / Source method: isolated from a natural source / Formula: H2O
Compound detailsThe peptide linker connects the variable light chain and the variable heavy chain.
Sequence detailsNeither the sequence of the wild-type nor the mutated sequence, from which the structure was ...Neither the sequence of the wild-type nor the mutated sequence, from which the structure was solved, was deposited to a database. In comparison to the wild-type of the anti-his tag antibody 3d5 variable light chain, the mutated sequence chain L has the following mutations: L9S, V78F, Y88D. In comparison to the wild-type of the anti-his tag antibody 3d5 variable heavy chain, the mutated sequence chain H has the following mutations: L12D, H48P, S51G, K77R, E100D, L144T. The first three residues DYK, are part of the flag recognition tag.

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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: 5.4 Å3/Da / Density % sol: 77 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.4
Details: PEG 8000, magnesium acetate, MES, pH 6.4, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
13.8 mg/mlprotein1drop
20.1 MMES1reservoirpH6.4
30.2 Mmagnesium acetate1reservoir
420 %(w/v)PEG80001reservoir
50.02 %(w/v)1reservoirNaN3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM1A / Wavelength: 0.873 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Oct 2, 2000 / Details: Mirrors
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. obs: 16996 / % possible obs: 99 % / Observed criterion σ(I): -2.5 / Redundancy: 7.54 % / Biso Wilson estimate: 52.8 Å2 / Rmerge(I) obs: 0.116 / Net I/σ(I): 16.6
Reflection shellResolution: 2.7→2.8 Å / Rmerge(I) obs: 0.537 / Mean I/σ(I) obs: 4.4 / % possible all: 99.8
Reflection
*PLUS
Lowest resolution: 30 Å / Redundancy: 7.6 % / Num. measured all: 128480

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: VL: PDB ENTRY 1TET, VH: PDB ENTRY 1PSK

1tet

1psk


Resolution: 2.7→30 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.222 996 -RANDOM
Rwork0.19 ---
all-17082 --
obs-16936 99.1 %-
Displacement parametersBiso mean: 33.4 Å2
Baniso -1Baniso -2Baniso -3
1-2.82 Å27.02 Å20 Å2
2--2.82 Å20 Å2
3----5.65 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.37 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1789 0 0 156 1945
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_improper_angle_deg0.8
X-RAY DIFFRACTIONc_dihedral_angle_deg26.8
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.024
RfactorNum. reflection% reflection
Rfree0.282 143 -
Rwork0.261 --
obs-2653 99.7 %
Refinement
*PLUS
Lowest resolution: 30 Å / Rfactor obs: 0.1904 / Rfactor Rfree: 0.222 / Rfactor Rwork: 0.1904
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0054
X-RAY DIFFRACTIONc_angle_deg1.3173
LS refinement shell
*PLUS
Highest resolution: 2.7 Å / Rfactor obs: 0.261

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