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- PDB-2jrt: NMR solution structure of the protein coded by gene RHOS4_12090 o... -

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Basic information

Entry
Database: PDB / ID: 2jrt
TitleNMR solution structure of the protein coded by gene RHOS4_12090 of Rhodobacter sphaeroides. Northeast Structural Genomics target RhR5
ComponentsUncharacterized protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / NMR Solution / NESG / PSI / target RhR5 / Rhodobacter sphaeroides / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homology
Function and homology information


sequence-specific DNA binding
Similarity search - Function
Protein of unknown function DUF1153 / Protein of unknown function (DUF1153) / Trp repressor/replication initiator / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DUF1153 domain-containing protein
Similarity search - Component
Biological speciesRhodobacter sphaeroides (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsWang, L. / Chen, C. / Nwosu, C. / Cunningham, K. / Owens, L. / Ma, L. / Xiao, R. / Liu, J. / Baran, M.C. / Swapna, G. ...Wang, L. / Chen, C. / Nwosu, C. / Cunningham, K. / Owens, L. / Ma, L. / Xiao, R. / Liu, J. / Baran, M.C. / Swapna, G. / Acton, T.B. / Rost, B. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: NMR solution structure of the protein coded by gene RHOS4_12090 of Rhodobacter sphaeroides.
Authors: Wang, L. / Montelione, G.T.
History
DepositionJun 28, 2007Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 21, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.3May 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: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)10,8781
Polymers10,8781
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)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Uncharacterized protein


Mass: 10877.595 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Strain: 2.4.1, NCIB 8253, DSM 158 / Gene: RHOS4_12090, RSP_2620 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): XL10 / References: UniProt: Q3J357

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1322D 1H-13C HSQC
1423D HNCA
1523D HNCO
1623D HN(CA)CB
1723D CBCA(CO)NH
1823D HBHA(CO)NH
1923D (H)CCH-TOCSY
11023D (H)CCH-COSY
1112CCH-TOCSY
11213D 1H-15N NOESY
11323D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.0 mM [U-5% 13C; U-100% 15N] protein, 10 mM DTT, 100 mM sodium chloride, 95% H2O/5% D2O95% H2O/5% D2O
21.0 mM [U-100% 13C; U-100% 15N] protein, 10 mM DTT, 100 mM sodium chloride, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMRhR5[U-5% 13C; U-100% 15N]1
10 mMDTT1
100 mMsodium chloride1
1.0 mMRhR5[U-100% 13C; U-100% 15N]2
10 mMDTT2
100 mMsodium chloride2
Sample conditionsIonic strength: 100 / pH: 6.5 / Pressure: ambient / Temperature: 293.0 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
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddarddata analysis
X-PLORBrungerstructure solution
PSVSBhattacharya and Montelionevalidation
X-PLORBrungerrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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