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- PDB-1vl3: DESIGN OF NEW MIMOCHROMES WITH UNIQUE TOPOLOGY -

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Basic information

Entry
Database: PDB / ID: 1vl3
TitleDESIGN OF NEW MIMOCHROMES WITH UNIQUE TOPOLOGY
ComponentsGLU-SER-GLN-LEU-HIS-SER-ASN-LYS-ARG
KeywordsDE NOVO PROTEIN / ALPHA-HELIX / DESIGN / MINIATURIZED METALLOPROTEINS
Function / homologyCO(III)-(DEUTEROPORPHYRIN IX)
Function and homology information
MethodSOLUTION NMR / MOLECULAR DYNAMIC SIMULATION FOR 400 PS
AuthorsLombardi, A. / Nastri, F. / Marasco, D. / Maglio, O. / De Sanctis, G. / Sinibaldi, F. / Santucci, R. / Coletta, M. / Pavone, V.
CitationJournal: Chemistry / Year: 2003
Title: Design of a New Mimochrome with Unique Topology.
Authors: Lombardi, A. / Nastri, F. / Marasco, D. / Maglio, O. / De Sanctis, G. / Sinibaldi, F. / Santucci, R. / Coletta, M. / Pavone, V.
History
DepositionJul 5, 2004Deposition site: RCSB / Processing site: RCSB
SupersessionJul 20, 2004ID: 1L1B
Revision 1.0Jul 20, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_conn / 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 / _pdbx_nmr_spectrometer.model / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GLU-SER-GLN-LEU-HIS-SER-ASN-LYS-ARG
B: GLU-SER-GLN-LEU-HIS-SER-ASN-LYS-ARG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,8183
Polymers2,2502
Non-polymers5681
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / -
Representative

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Components

#1: Protein/peptide GLU-SER-GLN-LEU-HIS-SER-ASN-LYS-ARG


Mass: 1125.240 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED.
#2: Chemical ChemComp-DEU / CO(III)-(DEUTEROPORPHYRIN IX)


Mass: 567.501 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H28CoN4O4

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121TOCSY
131DQF-COSY
NMR detailsText: THIS STRUCTURE WAS DETERMINED USING STANDARD 2D HOMONUCLEAR TECHNIQUES.

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Sample preparation

DetailsContents: 1MM CO(III)-MIMOCHROME IV 70% H2O, 30% CF3CD2OD
Sample conditionspH: 5.5 / Pressure: AMBIENT / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
DiscoverMSIrefinement
NMRPipestructure solution
Discoverstructure solution
RefinementMethod: MOLECULAR DYNAMIC SIMULATION FOR 400 PS / Software ordinal: 1
Details: THE STRUCTURE IS BASED ON A TOTAL OF 250 NOE-DERIVED DISTANCE RESTRAINTS
NMR ensembleConformers submitted total number: 1

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