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- PDB-2kik: An artificial di-iron oxo-protein with phenol oxidase activity -

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Basic information

Entry
Database: PDB / ID: 2kik
TitleAn artificial di-iron oxo-protein with phenol oxidase activity
ComponentsArtificial diiron protein
KeywordsDE NOVO PROTEIN / diiron proteins / four-heix bundle / de novo design / oxidase
Function / homologyImmunoglobulin FC, subunit C / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Function and homology information
MethodSOLUTION NMR / Energy restrained minimization
Model detailslowest energy, model 1
AuthorsMaglio, O. / Lombardi, A.
Citation
Journal: To be Published
Title: An artificial di-iron oxo-protein with phenol oxidase activity
Authors: Faiella, M. / Andreozzi, C. / Torres, R. / Pavone, V. / Maglio, O. / Nastri, F. / DeGrado, W.F. / Lombardi, A.
#1: Journal: J.Biol.Inorg.Chem. / Year: 2005
Title: Artificial di-iron proteins: solution characterization of four helix bundles containing two distinct types of inter-helical loops
Authors: Maglio, O. / Nastri, F. / Calhoun, J.R. / Lahr, S. / Wade, H. / Pavone, V. / DeGrado, W.F. / Lombardi, A.
#2: Journal: J.Am.Chem.Soc. / Year: 2005
Title: Response of a designed metalloprotein to changes in metal ion coordination, exogenous ligands, and active site volume determined by X-ray crystallography
Authors: Geremia, S. / Di Costanzo, L. / Randaccio, L. / Engel, D.E. / Lombardi, A. / Nastri, F. / DeGrado, W.F.
#3: Journal: Proc.Natl.Acad.Sci.USA / Year: 2003
Title: Preorganization of molecular binding sites in designed diiron proteins
Authors: Maglio, O. / Nastri, F. / Pavone, V. / Lombardi, A. / DeGrado, W.F.
History
DepositionMay 6, 2009Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Nov 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_conn_angle / 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 / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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: Artificial diiron protein
B: Artificial diiron protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,6724
Polymers11,5412
Non-polymers1312
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)30 / 40structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Artificial diiron protein


Mass: 5770.566 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Peptide synthesis
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR / Details: This protein was chemically synthesized
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H TOCSY
1212D 1H-1H NOESY
NMR detailsText: THIS STRUCTURE WAS DETERMINED USING STANDARD 2D HOMONUCLEAR TECHNIQUES

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Sample preparation

DetailsContents: 50mM sodium phosphate-1, 90% H2O/10% D2O / Solvent system: 90% H2O/10% D2O
SampleConc.: 50 mM / Component: sodium phosphate-1
Sample conditionspH: 6.0 / 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
NameVersionDeveloperClassification
TopSpin2.1Bruker Biospincollection
TopSpin2.1Bruker Biospinprocessing
XEASYBartels et al.data analysis
XEASYBartels et al.chemical shift assignment
XEASYBartels et al.peak picking
CYANA2.1Guntert, Mumenthaler, Wuthrichstructure solution
Amber7Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, Kollmrefinement
RefinementMethod: Energy restrained minimization / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 40 / Conformers submitted total number: 30 / Representative conformer: 1

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