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- PDB-5c2b: anti-CXCL13 parental scFv - 3B4 -

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Basic information

Entry
Database: PDB / ID: 5c2b
Titleanti-CXCL13 parental scFv - 3B4
ComponentsscFv 3B4
KeywordsIMMUNE SYSTEM / anti-CXCL13 / scFv
Function / homology
Function and homology information


immunoglobulin complex / immunoglobulin mediated immune response / antigen binding / extracellular region / plasma membrane
Similarity search - Function
Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold ...Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Immunoglobulin heavy variable 1-69D / IGH + IGL c465_light_IGLV2-14_IGLJ1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4049 Å
AuthorsTu, C. / Bard, J. / Mosyak, L.
CitationJournal: To Be Published
Title: Optimization of a scFv-based biotherapeutic by CDR side-chain clash repair
Authors: Tu, C. / Terrabube, V. / Tam, A. / Stochaj, W. / Fennell, B. / Lin, L. / Stahl, M. / LaVallie, E. / Somers, W. / Finlay, W. / Mosyak, L. / Bard, J. / Cunningham, O.
History
DepositionJun 15, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2017Group: Author supporting evidence / Derived calculations
Category: pdbx_struct_assembly_auth_evidence / pdbx_struct_oper_list
Item: _pdbx_struct_oper_list.symmetry_operation
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 / atom_site_anisotrop ...atom_site / atom_site_anisotrop / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_distant_solvent_atoms / 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_struct_special_symmetry / pdbx_unobs_or_zero_occ_residues / pdbx_validate_torsion / struct / struct_asym / struct_biol / struct_conf / struct_conn / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_sheet_range / struct_site / struct_site_gen
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 / _atom_site.occupancy / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_seq_id / _entity_poly_seq.entity_id / _entity_poly_seq.num / _entity_src_gen.entity_id / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_src_id / _pdbx_distant_solvent_atoms.auth_asym_id / _pdbx_distant_solvent_atoms.auth_seq_id / _pdbx_distant_solvent_atoms.neighbor_macromolecule_distance / _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_poly_seq_scheme.asym_id / _pdbx_poly_seq_scheme.entity_id / _pdbx_poly_seq_scheme.ndb_seq_num / _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_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_struct_special_symmetry.auth_asym_id / _pdbx_struct_special_symmetry.auth_seq_id / _pdbx_struct_special_symmetry.label_asym_id / _pdbx_unobs_or_zero_occ_residues.auth_asym_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_seq_id / _pdbx_validate_torsion.auth_asym_id / _pdbx_validate_torsion.auth_seq_id / _struct.pdbx_descriptor / _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_ref.db_code / _struct_ref.entity_id / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.pdbx_strand_id / _struct_ref_seq.seq_align_beg / _struct_ref_seq.seq_align_end / _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.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_seq_id / _struct_site_gen.auth_asym_id / _struct_site_gen.auth_comp_id / _struct_site_gen.auth_seq_id / _struct_site_gen.label_asym_id / _struct_site_gen.label_comp_id / _struct_site_gen.label_seq_id
Revision 3.0Jun 17, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations
Category: atom_site / pdbx_distant_solvent_atoms ...atom_site / pdbx_distant_solvent_atoms / pdbx_nonpoly_scheme / pdbx_struct_special_symmetry / struct_site / struct_site_gen
Item: _atom_site.auth_seq_id / _pdbx_distant_solvent_atoms.auth_seq_id ..._atom_site.auth_seq_id / _pdbx_distant_solvent_atoms.auth_seq_id / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_struct_special_symmetry.auth_seq_id / _struct_site.details / _struct_site.pdbx_auth_seq_id / _struct_site_gen.auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: scFv 3B4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6664
Polymers26,5601
Non-polymers1063
Water6,449358
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area390 Å2
ΔGint-27 kcal/mol
Surface area11300 Å2
Unit cell
Length a, b, c (Å)131.900, 133.500, 44.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11H-1320-

HOH

21H-1440-

HOH

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Components

#1: Antibody scFv 3B4


Mass: 26559.936 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: HEK293 / Gene: IGHV1-69D, IGHV1-69-2 / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: A0A0B4J2H0, UniProt: A0A5C2GBJ8
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 358 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.6 Å3/Da / Density % sol: 66 % / Description: very nice brick like
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: The concentration of 3B4 was 11 mg/ml in 20 mM Tris, pH 7.5 and 150 mM NaCl. Each drop contained 0.15 ul 3B4 and 0.15 ul reservoir solution containing 100 mM HEPES, pH 7.5 and 4300 mM NaCl.

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 2, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4049→50 Å / Num. obs: 77347 / % possible obs: 99.9 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.037 / Net I/σ(I): 22.5
Reflection shellResolution: 1.4049→1.48 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.542 / Mean I/σ(I) obs: 3 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
HKL-2000data reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: E10

Resolution: 1.4049→32.975 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1944 3850 4.98 %Random selection
Rwork0.1791 ---
obs0.1798 77314 99.68 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.4049→32.975 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1806 0 3 358 2167
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061976
X-RAY DIFFRACTIONf_angle_d1.0672716
X-RAY DIFFRACTIONf_dihedral_angle_d11.698729
X-RAY DIFFRACTIONf_chiral_restr0.079299
X-RAY DIFFRACTIONf_plane_restr0.004352
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4049-1.42210.28661350.26462475X-RAY DIFFRACTION96
1.4221-1.44010.27481390.2432620X-RAY DIFFRACTION100
1.4401-1.4590.26971310.2462562X-RAY DIFFRACTION100
1.459-1.4790.28081420.23322603X-RAY DIFFRACTION100
1.479-1.50010.25231320.22492615X-RAY DIFFRACTION100
1.5001-1.52250.25521300.21722574X-RAY DIFFRACTION100
1.5225-1.54630.26731440.21032660X-RAY DIFFRACTION100
1.5463-1.57170.25031380.212571X-RAY DIFFRACTION100
1.5717-1.59880.23041350.20122620X-RAY DIFFRACTION100
1.5988-1.62780.22161360.19952597X-RAY DIFFRACTION100
1.6278-1.65920.22031390.18942627X-RAY DIFFRACTION100
1.6592-1.6930.19411370.18272579X-RAY DIFFRACTION100
1.693-1.72980.22431330.18622653X-RAY DIFFRACTION100
1.7298-1.77010.17771440.18162581X-RAY DIFFRACTION100
1.7701-1.81430.20261310.18562618X-RAY DIFFRACTION100
1.8143-1.86340.21761400.1812623X-RAY DIFFRACTION100
1.8634-1.91820.17931360.17632615X-RAY DIFFRACTION100
1.9182-1.98010.2011400.17462622X-RAY DIFFRACTION100
1.9801-2.05090.18291360.16732652X-RAY DIFFRACTION100
2.0509-2.1330.16561350.1682650X-RAY DIFFRACTION100
2.133-2.230.20691380.17522616X-RAY DIFFRACTION100
2.23-2.34760.19481390.18882635X-RAY DIFFRACTION100
2.3476-2.49460.16831400.19062637X-RAY DIFFRACTION100
2.4946-2.68710.20241340.19442638X-RAY DIFFRACTION100
2.6871-2.95740.20231390.18832667X-RAY DIFFRACTION100
2.9574-3.3850.19811380.18512667X-RAY DIFFRACTION100
3.385-4.26330.17641420.14392684X-RAY DIFFRACTION99
4.2633-32.98410.16811470.16442803X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)DetailsOrigin x (Å)Origin y (Å)Origin z (Å)
11.2805-1.5347-0.85314.01721.55311.6197-0.0341-0.0129-0.17560.1706-0.07060.27770.1808-0.13030.1030.15780.01670.01170.16510.00190.1405scFv heavy chain34.822319.120911.8111
22.86450.1904-0.41381.7781-0.34121.20410.06280.0247-0.0222-0.0412-0.00320.1022-0.02320.0083-0.0450.09210.02840.01220.08930.00720.1006scFv light chain55.10614.56849.3845
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain H
2X-RAY DIFFRACTION2chain L

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