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- PDB-1u7m: Solution structure of a diiron protein model: Due Ferri(II) turn ... -

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Entry
Database: PDB / ID: 1u7m
TitleSolution structure of a diiron protein model: Due Ferri(II) turn mutant
ComponentsFour-helix bundle model
KeywordsDE NOVO PROTEIN / Diiron proteins / four-helix bundle / protein design / inter-helical loops
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
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / Torsion Angle Dynamics, Simulated Annealing, Energy Restrained Minimization
AuthorsMaglio, O. / Nastri, F. / Calhoun, J.R. / Lahr, S. / Pavone, V. / DeGrado, W.F. / Lombardi, A.
Citation
Journal: J.Mol.Biol. / Year: 2005
Title: Analysis and Design of Turns in alpha-Helical Hairpins
Authors: Lahr, S.J. / Engel, D.E. / Stayrook, S.E. / Maglio, O. / North, B. / Geremia, S. / Lombardi, A. / Degrado, W.F.
#1: Journal: To be Published
Title: Solution characterization of diiron proteins containing two distinct types of inter-helical loops
Authors: Maglio, O. / Nastri, F. / Calhoun, J.R. / Lahr, S. / Pavone, V. / DeGrado, W.F. / Lombardi, A.
#2: Journal: Protein Sci. / Year: 2001
Title: Proton and metal ion-dependent assembly of a model diiron protein
Authors: Pasternak, A. / Kaplan, J. / Lear, J.D. / DeGrado, W.F.
#3: Journal: Proc.Natl.Acad.Sci.USA / Year: 2000
Title: Inaugural article: retrostructural analysis of metalloproteins: application to the design of a minimal model for diiron proteins
Authors: Lombardi, A. / Summa, C.M. / Geremia, S. / Randaccio, L. / Pavone, V. / DeGrado, W.F.
#4: 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
DepositionAug 4, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 1, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 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.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
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Four-helix bundle model
B: Four-helix bundle model
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,0864
Polymers12,9552
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)20 / 40structures with the least restraint violations, structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Four-helix bundle model


Mass: 6477.396 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PET28A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3)
#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
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D TOCSY
121DQF-COSY
1312D NOESY
NMR detailsText: This structure was determined using standard 2D homonuclear technique

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Sample preparation

DetailsContents: 0.5mM protein concentration; 50mM phosphate buffer; 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 50mm phosphate buffer / pH: 6.1 / Pressure: Ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe1.7Delaglio et al.processing
DYANA1.5Guentert et al.structure solution
Amber7Case et al.refinement
RefinementMethod: Torsion Angle Dynamics, Simulated Annealing, Energy Restrained Minimization
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations, structures with the lowest energy
Conformers calculated total number: 40 / Conformers submitted total number: 20

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