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- PDB-2mi7: Solution NMR structure of alpha3Y -

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Basic information

Entry
Database: PDB / ID: 2mi7
TitleSolution NMR structure of alpha3Y
Componentsde novo protein a3Y
KeywordsDE NOVO PROTEIN / three-helix bundle / redox protein / tyrosine radical / proton-coupled electron transfer
Function / homologyDesigned single chain three-helix bundle / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / Up-down Bundle / Mainly Alpha
Function and homology information
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / simulated annealing
AuthorsGlover, S.D. / Jorge, C. / Liang, L. / Valentine, K.G. / Hammarstrom, L. / Tommos, C.
Citation
Journal: J.Am.Chem.Soc. / Year: 2014
Title: Photochemical tyrosine oxidation in the structurally well-defined alpha 3Y protein: proton-coupled electron transfer and a long-lived tyrosine radical.
Authors: Glover, S.D. / Jorge, C. / Liang, L. / Valentine, K.G. / Hammarstrom, L. / Tommos, C.
#1: Journal: Biochemistry / Year: 1999
Title: De novo proteins as models of radical enzymes.
Authors: Tommos, C. / Skalicky, J.J. / Pilloud, D.L. / Wand, A.J. / Dutton, P.L.
#2: Journal: J.Am.Chem.Soc. / Year: 2002
Title: Structure of a de novo designed protein model of radical enzymes.
Authors: Dai, Q.H. / Tommos, C. / Fuentes, E.J. / Blomberg, M.R. / Dutton, P.L. / Wand, A.J.
#3: Journal: J.Am.Chem.Soc. / Year: 2011
Title: Electrochemical and structural properties of a protein system designed to generate tyrosine Pourbaix diagrams.
Authors: Martinez-Rivera, M.C. / Berry, B.W. / Valentine, K.G. / Westerlund, K. / Hay, S. / Tommos, C.
#4: Journal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Reversible voltammograms and a Pourbaix diagram for a protein tyrosine radical.
Authors: Berry, B.W. / Martinez-Rivera, M.C. / Tommos, C.
#5: Journal: Biochemistry / Year: 2013
Title: Reversible phenol oxidation and reduction in the structurally well-defined 2-Mercaptophenol-alpha 3C protein.
Authors: Tommos, C. / Valentine, K.G. / Martinez-Rivera, M.C. / Liang, L. / Moorman, V.R.
History
DepositionDec 10, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 20, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 27, 2014Group: Database references
Revision 1.2Jan 14, 2015Group: Database references
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.4May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: de novo protein a3Y


Theoretical massNumber of molelcules
Total (without water)7,5401
Polymers7,5401
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)32 / 1000NOE violation cutoff >0.1A, bb dihedral angle violation cutoff >2 degrees, then lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein de novo protein a3Y


Mass: 7539.863 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Plasmid: pET32b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIL

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-13C HSQC
1313D HNCO
1413D HN(CA)CO
1513D CBCA(CO)NH
1613D HN(CA)CB
1713D H(CC)(CO)NH TOCSY
1813D CC(CO)NH TOCSY
1923D (H)CCH-TOCSY
11023D (H)CCH3-TOCSY
11122D 1H-1H NOESY aromatic
11223D 1H-13C NOESY aromatic
11313D 1H-15N NOESY
11414D 1H-15N NOESY
11524D 1H-13C NOESY
11632D 1H-13C HSQC
11722D 1H-13C HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
10.95 mM [U-100% 13C; U-100% 15N] a3Y, 30 mM [U-100% 2H] sodium acetate, 30 mM sodium chloride, 0.25 mM DSS, 0.02 % (w/v) sodium azide, 92% H2O/8% D2O92% H2O/8% D2O
20.95 mM [U-100% 13C; U-100% 15N] a3Y, 30 mM [U-100% 2H] sodium acetate, 30 mM sodium chloride, 0.25 mM DSS, 0.02 % (w/v) sodium azide, 99.99% D2O99.99% D2O
30.95 mM [U-10% 13C; U-100% 15N] a3Y, 30 mM [U-100% 2H] sodium acetate, 30 mM sodium chloride, 0.25 mM DSS, 0.02 % (w/v) sodium azide, 99.99% D2O99.99% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.95 mMa3Y-1[U-100% 13C; U-100% 15N]1
30 mMsodium acetate-2[U-100% 2H]1
30 mMsodium chloride-31
0.25 mMDSS-41
0.02 %sodium azide-51
0.95 mMa3Y-6[U-100% 13C; U-100% 15N]2
30 mMsodium acetate-7[U-100% 2H]2
30 mMsodium chloride-82
0.25 mMDSS-92
0.02 %sodium azide-102
0.95 mMa3Y-11[U-10% 13C; U-100% 15N]3
30 mMsodium acetate-12[U-100% 2H]3
30 mMsodium chloride-133
0.25 mMDSS-143
0.02 %sodium azide-153
Sample conditionsIonic strength: 60 / pH: 5.6 / Pressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE7501
Bruker AvanceBrukerAVANCE5002

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Processing

NMR software
NameVersionDeveloperClassification
TopSpinBruker Biospincollection
FelixAccelrys Software Inc.processing
Sparky3.113Goddardchemical shift assignment
Sparky3.113Goddardpeak picking
Sparky3.113Goddardnoe integration
TALOS+Cornilescu, Delaglio and Baxsecondary structure analysis
CNS1.21Brunger, Adams, Clore, Gros, Nilges and Readstructure calculation
CNS1.21Brunger, Adams, Clore, Gros, Nilges and Readrefinement
PSVS1.5Bhattacharya and Montelionestructure evaluation
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 784 / NOE intraresidue total count: 221 / NOE long range total count: 165 / NOE medium range total count: 214 / NOE sequential total count: 184 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 54 / Protein psi angle constraints total count: 52
NMR representativeSelection criteria: lowest energy
NMR ensembleAverage torsion angle constraint violation: 0.153 °
Conformer selection criteria: NOE violation cutoff >0.1A, bb dihedral angle violation cutoff >2 degrees, then lowest energy
Conformers calculated total number: 1000 / Conformers submitted total number: 32 / Maximum lower distance constraint violation: 0 Å / Maximum torsion angle constraint violation: 1.037 ° / Maximum upper distance constraint violation: 0.094 Å / Torsion angle constraint violation method: sum of r^-6
NMR ensemble rmsDistance rms dev: 0.0058 Å / Distance rms dev error: 0.0005 Å

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