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- PDB-2lxy: NMR structure of 2-MERCAPTOPHENOL-ALPHA3C -

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Basic information

Entry
Database: PDB / ID: 2lxy
TitleNMR structure of 2-MERCAPTOPHENOL-ALPHA3C
Components2-mercaptophenol-alpha3C
KeywordsDE NOVO PROTEIN / three-helix bundle / redox protein / phenol oxidation-reduction / 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 / 2-MERCAPTOPHENOL
Function and homology information
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsTommos, C. / Valentine, K.G. / Martinez-Rivera, M.C. / Liang, L. / Moorman, V.R.
Citation
Journal: Biochemistry / Year: 2013
Title: Reversible phenol oxidation and reduction in the structurally well-defined 2-Mercaptophenol-alpha(3)C protein.
Authors: Tommos, C. / Valentine, K.G. / Martinez-Rivera, M.C. / Liang, L. / Moorman, V.R.
#1: 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.
#2: 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.
#3: Journal: Biochemistry / Year: 2005
Title: Moving a phenol hydroxyl group from the surface to the interior of a protein: effects on the phenol potential and pK(A).
Authors: Hay, S. / Westerlund, K. / Tommos, C.
#4: 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.
#5: 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.
#6: Journal: Biochemistry / Year: 1999
Title: De novo proteins as models of radical enzymes
Authors: Tommos, C. / Skalicky, J.J. / Pilloud, D.L. / Wand, A. / Dutton, P.
History
DepositionSep 6, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 27, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / struct_conn / struct_site
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 / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 27, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 2-mercaptophenol-alpha3C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,6062
Polymers7,4801
Non-polymers1261
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 / 1000structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein 2-mercaptophenol-alpha3C


Mass: 7479.832 Da / Num. of mol.: 1 / Source method: obtained synthetically / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-HTS / 2-MERCAPTOPHENOL / 2-HYDROXYTHIOPHENOL


Mass: 126.176 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H6OS
Has protein modificationY

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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 HNHA
1513D CBCA(CO)NH
1613D HN(CA)CB
1713D H(CC)(CO)NH TOCSY
1813D CC(CO)NH TOCSY
1923D (H)CCH-TOCSY
11023D 1H-13C NOESY
11113D 1H-15N NOESY
11242D 1H-1H NOESY
11324D 1H-13C NOESY
11432D 1H-13C HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
10.8 mM [U-100% 13C; U-100% 15N] 2-mercaptophenol-alpha3C, 30 mM [U-100% 2H] sodium acetate, 30 mM potassium chloride, 0.25 mM DSS, 90% H2O/10% D2O90% H2O/10% D2O
20.8 mM [U-100% 13C; U-100% 15N] 2-mercaptophenol-alpha3C, 30 mM [U-100% 2H] sodium acetate, 30 mM potassium chloride, 0.25 mM DSS, 99.99% D2O99.99% D2O
30.8 mM [U-10% 13C; U-100% 15N] 2-mercaptophenol-alpha3C, 30 mM [U-100% 2H] sodium acetate, 30 mM potassium chloride, 0.25 mM DSS, 99.99% D2O99.99% D2O
40.8 mM 2-mercaptophenol-alpha3C, 30 mM [U-100% 2H] sodium acetate, 30 mM potassium chloride, 0.25 mM DSS, 99.99% D2O99.99% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.8 mM2-mercaptophenol-alpha3C-1[U-100% 13C; U-100% 15N]1
30 mMsodium acetate-2[U-100% 2H]1
30 mMpotassium chloride-31
0.25 mMDSS-41
0.8 mM2-mercaptophenol-alpha3C-5[U-100% 13C; U-100% 15N]2
30 mMsodium acetate-6[U-100% 2H]2
30 mMpotassium chloride-72
0.25 mMDSS-82
0.8 mM2-mercaptophenol-alpha3C-9[U-10% 13C; U-100% 15N]3
30 mMsodium acetate-10[U-100% 2H]3
30 mMpotassium chloride-113
0.25 mMDSS-123
0.8 mM2-mercaptophenol-alpha3C-134
30 mMsodium acetate-14[U-100% 2H]4
30 mMpotassium chloride-154
0.25 mMDSS-164
Sample conditionsIonic strength: 60 / pH: 5.5 / Pressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 750 MHz

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
FelixAccelrys Software Inc.processing
SparkyGoddardchemical shift assignment
SparkyGoddarddata analysis
SparkyGoddardpeak picking
SparkyGoddardnoe integration
TALOSCornilescu, Delaglio and Baxsecondary structure analysis
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure calculation
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 1000 / Conformers submitted total number: 32

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