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- PDB-5nsc: Fc DEKK heterodimer variant -

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Basic information

Entry
Database: PDB / ID: 5nsc
TitleFc DEKK heterodimer variant
Components
  • (Putative uncharacterized protein ...) x 2
  • Fc-III peptide
KeywordsIMMUNE SYSTEM / IgG / Fc heterodimer / L351D/L368E + L351K/T366K
Function / homology
Function and homology information


immunoglobulin complex, circulating / immunoglobulin receptor binding / complement activation, classical pathway / antigen binding / antibacterial humoral response / blood microparticle / extracellular exosome / metal ion binding / plasma membrane
Similarity search - Function
Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain ...Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Uncharacterized protein DKFZp686C11235
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsDe Nardis, C. / Hendriks, L.J.A. / Poirier, E. / Arvinte, T. / Gros, P. / Bakker, A.B.H. / de Kruif, J.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
European Union Seventh Framework Programme (FP7/2007-2013)283570 Netherlands
CitationJournal: J. Biol. Chem. / Year: 2017
Title: A new approach for generating bispecific antibodies based on a common light chain format and the stable architecture of human immunoglobulin G1.
Authors: De Nardis, C. / Hendriks, L.J.A. / Poirier, E. / Arvinte, T. / Gros, P. / Bakker, A.B.H. / de Kruif, J.
History
DepositionApr 26, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 5, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 12, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Sep 13, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / diffrn_radiation_wavelength / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_chiral / pdbx_validate_close_contact / struct_asym / struct_conn / 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_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _database_PDB_caveat.text / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative uncharacterized protein DKFZp686C11235
B: Putative uncharacterized protein DKFZp686C11235
C: Fc-III peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,7987
Polymers53,7703
Non-polymers3,0294
Water3,351186
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8870 Å2
ΔGint52 kcal/mol
Surface area22200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.059, 65.442, 78.710
Angle α, β, γ (deg.)90.00, 103.24, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Putative uncharacterized protein ... , 2 types, 2 molecules AB

#1: Protein Putative uncharacterized protein DKFZp686C11235


Mass: 26186.682 Da / Num. of mol.: 1 / Mutation: L351K, T366K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: HEK-293 / Gene: DKFZp686C11235 / Production host: Homo sapiens (human) / References: UniProt: Q6MZV7
#2: Protein Putative uncharacterized protein DKFZp686C11235


Mass: 26049.238 Da / Num. of mol.: 1 / Mutation: L351D, L368E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: HEK-293 / Gene: DKFZp686C11235 / Production host: Homo sapiens (human) / References: UniProt: Q6MZV7

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Protein/peptide / Sugars , 2 types, 3 molecules C

#3: Protein/peptide Fc-III peptide


Mass: 1533.749 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others)
#4: Polysaccharide beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose- ...beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1422.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-4DGlcpNAcb1-2DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/5,8,7/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a2112h-1b_1-5][a1221m-1a_1-5]/1-1-2-3-3-1-4-5/a4-b1_a6-h1_b4-c1_c3-d1_c6-e1_e2-f1_f4-g1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}}}}[(6+1)][b-L-Fucp]{}}}LINUCSPDB-CARE

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Non-polymers , 2 types, 188 molecules

#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / 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: 2.94 Å3/Da / Density % sol: 58.19 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.2 M sodium fluoride, 20% w/v PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 7, 2016
RadiationMonochromator: liquid nitrogen cooled channel-cut silicon monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.3→76.62 Å / Num. obs: 26379 / % possible obs: 98.7 % / Redundancy: 2.8 % / Biso Wilson estimate: 38.55 Å2 / CC1/2: 0.972 / Rmerge(I) obs: 0.154 / Rpim(I) all: 0.106 / Net I/σ(I): 3.6
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.531 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2511 / CC1/2: 0.565 / Rpim(I) all: 0.367 / % possible all: 95.4

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DK0

5dk0


Resolution: 2.3→76.619 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2647 1279 4.85 %
Rwork0.2254 --
obs0.2273 26344 98.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→76.619 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3450 0 204 186 3840
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033784
X-RAY DIFFRACTIONf_angle_d0.7255169
X-RAY DIFFRACTIONf_dihedral_angle_d11.2191455
X-RAY DIFFRACTIONf_chiral_restr0.029606
X-RAY DIFFRACTIONf_plane_restr0.003636
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.39210.32061310.30382809X-RAY DIFFRACTION99
2.3921-2.5010.3181560.29132765X-RAY DIFFRACTION99
2.501-2.63280.30981360.28942770X-RAY DIFFRACTION99
2.6328-2.79780.30541450.27732706X-RAY DIFFRACTION98
2.7978-3.01380.29981190.27662816X-RAY DIFFRACTION99
3.0138-3.31710.28041420.24192771X-RAY DIFFRACTION99
3.3171-3.79710.27451530.2192798X-RAY DIFFRACTION99
3.7971-4.78390.22421460.18022788X-RAY DIFFRACTION99
4.7839-76.66180.22971510.1822842X-RAY DIFFRACTION98
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)Origin x (Å)Origin y (Å)Origin z (Å)
11.87190.29190.59032.51820.40813.81770.152-0.16750.01370.1751-0.22310.36280.4002-0.30850.07450.3475-0.1256-0.01130.27750.03170.38182.635525.39217.1655
23.1994-1.078-0.68094.3881-1.22721.93740.00850.34490.1446-0.1284-0.0622-0.10990.024-0.04890.05590.2698-0.0125-0.00720.3118-0.00910.1346-9.723921.6208-23.6021
32.7816-0.92131.25582.0999-1.38795.05390.04640.02290.07690.0899-0.0783-0.1151-0.12680.08730.05240.2508-0.01010.06360.182-0.02880.3304-32.41494.157.2039
42.6924-0.8639-0.07244.41781.29513.10120.01510.5159-0.1976-0.23460.04070.03510.07330.0496-0.01620.2431-0.0620.00230.3436-0.0420.1671-20.67388.3722-23.672
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and ((resseq 238:341))
2X-RAY DIFFRACTION2chain 'A' and ((resseq 342:444))
3X-RAY DIFFRACTION3chain 'B' and ((resseq 238:341))
4X-RAY DIFFRACTION4chain 'B' and ((resseq 342:444))

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