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- PDB-5us3: Heterogeneous-backbone Foldamer Mimic of the Sp1-3 Zinc Finger -

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Entry
Database: PDB / ID: 5us3
TitleHeterogeneous-backbone Foldamer Mimic of the Sp1-3 Zinc Finger
ComponentsHeterogeneous-Backbone Variant of the Sp1-3 Zinc Finger: N-Me-Ala3, N-Me-Arg10, beta-3-Asp15, beta-3-Lys19, beta3-Lys22, beta-3-Gln25
KeywordsDE NOVO PROTEIN / zinc finger / heterogeneous backbone / foldamer
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsGeorge, K.L. / Horne, W.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM107161 United States
CitationJournal: J. Am. Chem. Soc. / Year: 2017
Title: Heterogeneous-Backbone Foldamer Mimics of Zinc Finger Tertiary Structure.
Authors: George, K.L. / Horne, W.S.
History
DepositionFeb 13, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 31, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 21, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Data collection
Category: pdbx_audit_support / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _pdbx_audit_support.funding_organization / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.4Jun 14, 2023Group: Database references / Derived calculations / Other / Category: database_2 / pdbx_database_status / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_validate_main_chain_plane / pdbx_validate_peptide_omega / pdbx_validate_rmsd_angle / pdbx_validate_torsion
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id
Revision 2.1Jul 10, 2024Group: Data collection / Database references / Category: chem_comp / database_2 / Item: _chem_comp.type / _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Heterogeneous-Backbone Variant of the Sp1-3 Zinc Finger: N-Me-Ala3, N-Me-Arg10, beta-3-Asp15, beta-3-Lys19, beta3-Lys22, beta-3-Gln25
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,5502
Polymers3,4841
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area100 Å2
ΔGint0 kcal/mol
Surface area2970 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)9 / 200structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Heterogeneous-Backbone Variant of the Sp1-3 Zinc Finger: N-Me-Ala3, N-Me-Arg10, beta-3-Asp15, beta-3-Lys19, beta3-Lys22, beta-3-Gln25


Mass: 3484.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D TOCSY
121isotropic12D COSY
131isotropic12D NOESY

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Sample preparation

DetailsType: solution
Contents: 0.2 mM NA DSS, 1.5 mM NA zinc chloride, 1.25 mM NA peptide, 9:1 H2O/D2O
Label: sample / Solvent system: 9:1 H2O/D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.2 mMDSSNA1
1.5 mMzinc chlorideNA1
1.25 mMpeptideNA1
Sample conditionsIonic strength: 5 mM / Label: conditions / pH: 7.0 Not defined / Pressure: 1 atm / Temperature: 277 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 700 MHz

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Processing

NMR software
NameVersionDeveloperClassification
TopSpinBruker Biospincollection
SparkyGoddarddata analysis
CNS1.3Brunger, Adams, Clore, Gros, Nilges and Readrefinement
CNS1.3Brunger, Adams, Clore, Gros, Nilges and Readstructure calculation
RefinementMethod: simulated annealing / Software ordinal: 7
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 200 / Conformers submitted total number: 9

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