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- PDB-5w8z: Solution Structure of XPH2, a Hybrid Sequence of Xfaso 1 and Pfl ... -

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Basic information

Entry
Database: PDB / ID: 5w8z
TitleSolution Structure of XPH2, a Hybrid Sequence of Xfaso 1 and Pfl 6, Two Cro Proteins With Different Folds
ComponentsXPH2
KeywordsTRANSCRIPTION / helix-turn-helix / structural evolution / conformational switch / metamorphic protein / disulfide bond / transcription factor
Function / homologylambda repressor-like DNA-binding domains / 434 Repressor (Amino-terminal Domain) / Orthogonal Bundle / Mainly Alpha
Function and homology information
Biological speciesPseudomonas fluorescens PF5 (bacteria)
MethodSOLUTION NMR / CYANA
AuthorsKumirov, V.K. / Dykstra, E.M. / Cordes, M.H.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM066806 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM104040 United States
CitationJournal: Protein Sci. / Year: 2018
Title: Multistep mutational transformation of a protein fold through structural intermediates.
Authors: Kumirov, V.K. / Dykstra, E.M. / Hall, B.M. / Anderson, W.J. / Szyszka, T.N. / Cordes, M.H.J.
History
DepositionJun 22, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 11, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 8, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Nov 7, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / pdbx_nmr_software
Item: _pdbx_audit_support.funding_organization / _pdbx_nmr_software.name
Revision 1.4Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: XPH2


Theoretical massNumber of molelcules
Total (without water)7,8881
Polymers7,8881
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Monomer confirmed by SEC (gel filtration)
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100lowest energy
RepresentativeModel #1lowest energy
DetailsMonomer confirmed by SEC (gel filtration)

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Components

#1: Protein XPH2


Mass: 7887.996 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Hybrid between two natural Cro sequences from prophages in Xylella fastidiosa and Pseudomonas fluorescens
Source: (gene. exp.) Pseudomonas fluorescens PF5 (bacteria) / Gene: CRO / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
113isotropic13D 15N-separated NOESY
122isotropic13D 13C-separated NOESY
131isotropic13D HNCO
141isotropic13D HN(CA)CB
151isotropic13D CBCA(CO)NH
161isotropic13D (H)CCH-TOCSY
174isotropic12D 1H-13C HSQC aliphatic
183isotropic12D 1H-15N HSQC

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.8 mM [U-13C; U-15N] XPH2, 50 mM NA- potassium phosphate, 150 mM NA- potassium chloride, 0.01 % NA- sodium azide, 0.1 mM NA- DSS, 1 M [U-2H] trimethylamine oxide, 90% H2O/10% D2O13C_15N_sample90% H2O/10% D2O
solution41.6 mM [U-10% 13C] XPH2, 50 mM NA- potassium phosphate, 150 mM NA- potassium chloride, 0.01 % NA- sodium azide, 0.1 mM NA- DSS, 90% H2O/10% D2O10% 13C sample90% H2O/10% D2O
solution30.9 mM [U-15N] XPH2, 50 mM NA- potassium phosphate, 150 mM NA- potassium chloride, 0.01 % NA- sodium azide, 0.1 mM NA- DSS, 90% H2O/10% D2O15N_sample90% H2O/10% D2O
solution20.6 mM [U-13C; U-15N] XPH2, 50 mM NA- potassium phosphate, 150 mM NA- potassium chloride, 0.01 % NA- sodium azide, 0.1 mM NA- DSS, 1 M [U-2H] trimethylamine oxide, 100% D2O13C_15N_sample_D20100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.8 mMXPH2[U-13C; U-15N]1
50 mMpotassium phosphateNA-1
150 mMpotassium chlorideNA-1
0.01 %sodium azideNA-1
0.1 mMDSSNA-1
1 Mtrimethylamine oxide[U-2H]1
1.6 mMXPH2[U-10% 13C]4
50 mMpotassium phosphateNA-4
150 mMpotassium chlorideNA-4
0.01 %sodium azideNA-4
0.1 mMDSSNA-4
0.9 mMXPH2[U-15N]3
50 mMpotassium phosphateNA-3
150 mMpotassium chlorideNA-3
0.01 %sodium azideNA-3
0.1 mMDSSNA-3
0.6 mMXPH2[U-13C; U-15N]2
50 mMpotassium phosphateNA-2
150 mMpotassium chlorideNA-2
0.01 %sodium azideNA-2
0.1 mMDSSNA-2
1 Mtrimethylamine oxide[U-2H]2
Sample conditionsIonic strength: 150 mM / Label: conditions_1 / pH: 6.5 pH* / Pressure: 1 atm / Temperature: 293 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
CNSBrunger A. T. et.al.refinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: CYANA / Software ordinal: 1
Details: Water refinement of the lowest energy 20 structures was performed using CNS
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: lowest energy / Conformers calculated total number: 100 / Conformers submitted total number: 20

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