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- PDB-1k09: Solution structure of BetaCore, A Designed Water Soluble Four-Str... -

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Basic information

Entry
Database: PDB / ID: 1k09
TitleSolution structure of BetaCore, A Designed Water Soluble Four-Stranded Antiparallel b-sheet Protein
Components
  • Core Module I
  • Core Module II
KeywordsDE NOVO PROTEIN / FOUR-STRANDED ANTIPARALLEL BETA-SHEET
Function / homology
Function and homology information


trypsinogen activation / negative regulation of serine-type endopeptidase activity / sulfate binding / potassium channel inhibitor activity / negative regulation of platelet aggregation / zymogen binding / molecular function inhibitor activity / negative regulation of thrombin-activated receptor signaling pathway / serine protease inhibitor complex / serine-type endopeptidase inhibitor activity ...trypsinogen activation / negative regulation of serine-type endopeptidase activity / sulfate binding / potassium channel inhibitor activity / negative regulation of platelet aggregation / zymogen binding / molecular function inhibitor activity / negative regulation of thrombin-activated receptor signaling pathway / serine protease inhibitor complex / serine-type endopeptidase inhibitor activity / protease binding / calcium ion binding / extracellular space
Similarity search - Function
: / Proteinase inhibitor I2, Kunitz, conserved site / Pancreatic trypsin inhibitor (Kunitz) family signature. / BPTI/Kunitz family of serine protease inhibitors. / Pancreatic trypsin inhibitor Kunitz domain / Kunitz/Bovine pancreatic trypsin inhibitor domain / Pancreatic trypsin inhibitor (Kunitz) family profile. / Pancreatic trypsin inhibitor Kunitz domain superfamily
Similarity search - Domain/homology
: / Pancreatic trypsin inhibitor
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodSOLUTION NMR / simulated annealing
AuthorsCarulla, N. / Woodward, C. / Barany, G.
CitationJournal: Protein Sci. / Year: 2002
Title: BetaCore, a designed water soluble four-stranded antiparallel beta-sheet protein.
Authors: Carulla, N. / Woodward, C. / Barany, G.
History
DepositionSep 18, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.0Nov 15, 2023Group: Advisory / Atomic model / Data collection
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_database_remark
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id / _pdbx_database_remark.text
Revision 3.0Feb 21, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / diffrn / diffrn_radiation / diffrn_radiation_wavelength / entity / entity_name_com / entity_poly / entity_poly_seq / pdbx_database_remark / pdbx_entity_nonpoly / pdbx_entity_src_syn / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_struct_mod_residue / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / pdbx_validate_torsion / struct / struct_asym / struct_conn / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._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.group_PDB / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity_poly.pdbx_seq_one_letter_code / _entity_poly_seq.mon_id / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_common_name / _pdbx_entity_src_syn.organism_scientific / _pdbx_entity_src_syn.pdbx_beg_seq_num / _pdbx_entity_src_syn.pdbx_end_seq_num / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_oper_list.symmetry_operation / _pdbx_validate_torsion.auth_comp_id / _struct.pdbx_model_details / _struct_ref.pdbx_align_begin / _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.seq_align_beg

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Core Module I
B: Core Module II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,9683
Polymers5,7072
Non-polymers2611
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200The submitted conformers are those with no constraint violations greater than 0.5 angstroms for NOEs and 5 degrees for dihedrals. They are also the ones with best covalent geometry.
RepresentativeModel #8closest to the average

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Components

#1: Protein/peptide Core Module I


Mass: 2831.340 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The peptide was chemically synthesized by solid-phase peptide chemistry. The sequence of the peptide is naturally found in Bos taurus (bovine).
Source: (synth.) Bos taurus (domestic cattle) / References: UniProt: P00974
#2: Protein/peptide Core Module II


Mass: 2875.376 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The peptide was chemically synthesized by solid-phase peptide chemistry. The sequence of the peptide is naturally found in Bos taurus (bovine).
Source: (synth.) Bos taurus (domestic cattle) / References: UniProt: P00974
#3: Chemical ChemComp-C55 / (7E)-4,9-dioxo-6-oxa-3,7,10-triazadodec-7-ene-1,12-dioic acid / CM II


Mass: 261.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H11N3O7
Sequence detailsThe sequence of these synthetic peptide (minus the modified amino acids and residue ASP 14) is ...The sequence of these synthetic peptide (minus the modified amino acids and residue ASP 14) is naturally found in Bovine Pancreatic Trypsin Inhibitor.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
2112D NOESY
2213D 15N-HSQC-NOESY
2313D 15N-HSQC-TOCSY
24115N-HSQC
15115N-HSQC
2612D TOCSY

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Sample preparation

DetailsContents: 0.4 mM BetaCore selectively-15N; pH3; 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditions
Conditions-IDpHPressure (kPa)Temperature (K)
13ambient 278 K
23ambient 288 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA8002

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.851Brungerstructure solution
NMRPipeDelaglioprocessing
NMRView5Johnsondata analysis
X-PLOR3.851Brungerrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: The structures are based on a total of 195 restraints, 172 are NOE-derived distance constraints, 14 dihedral angle restraints, 9 distance restraints from hydrogen bonds
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: The submitted conformers are those with no constraint violations greater than 0.5 angstroms for NOEs and 5 degrees for dihedrals. They are also the ones with best covalent geometry.
Conformers calculated total number: 200 / Conformers submitted total number: 20

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