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- PDB-1pbz: DE NOVO DESIGNED PEPTIDE-METALLOPORPHYRIN COMPLEX, SOLUTION STRUCTURE -

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Basic information

Entry
Database: PDB / ID: 1pbz
TitleDE NOVO DESIGNED PEPTIDE-METALLOPORPHYRIN COMPLEX, SOLUTION STRUCTURE
ComponentsDe novo designed cyclic peptide
KeywordsDE NOVO PROTEIN / PEPTIDE / METALLOPORPHYRIN / Heme / DE NOVO DESIGN
Function / homologyCOPROPORPHYRIN I CONTAINING CO(III)
Function and homology information
MethodSOLUTION NMR
AuthorsWang, J. / Rosenblatt, M.M. / Suslick, K.S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2003
Title: De novo designed cyclic-peptide heme complexes
Authors: Rosenblatt, M.M. / Wang, J. / Suslick, K.S.
History
DepositionMay 15, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 9, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_conn.conn_type_id / _struct_conn.id / _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_atom_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_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: De novo designed cyclic peptide
B: De novo designed cyclic peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,8833
Polymers3,1722
Non-polymers7121
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)14 / 40NO RESTRAINT VIOLATIONS GREATER THAN 0.3 ANGSTROMS
Representative

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Components

#1: Protein/peptide De novo designed cyclic peptide


Mass: 1585.807 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthesized by solid state methods
#2: Chemical ChemComp-PC3 / COPROPORPHYRIN I CONTAINING CO(III)


Mass: 711.626 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C36H36CoN4O8
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
NMR detailsText: IONIC_STRENGTH: 50mM PRESSURE: 1 ATM SOLVENT SYSTEM: AQUEOUS THE STRUCTURE WAS DETERMINED USING 2D HOMONUCLEAR METHODS (WUTHRICH, 1986) FOR RESONANCE ASSIGNMENTS GENERATION OF DISTANCE RESTRAINTS.

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Sample preparation

DetailsContents: 3mM cyclic peptide metalloporphyrin complex
Solvent system: pH 7.2, 50 mM potassium phosphate, 10 mM potassium chloride; 90% H2O/10%D2O
Sample conditionsIonic strength: 50 mM potassium phosphate, 10 mM potassium chloride
pH: 7.4 / Pressure: 1 atm / Temperature: 277 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Varian UNITY / Manufacturer: Varian / Model: UNITY / Field strength: 600 MHz

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Processing

NMR softwareName: Felix / Version: 98 / Developer: Accelrys, Inc / Classification: refinement
NMR ensembleConformer selection criteria: NO RESTRAINT VIOLATIONS GREATER THAN 0.3 ANGSTROMS
Conformers calculated total number: 40 / Conformers submitted total number: 14

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