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- PDB-2jtv: Solution Structure of protein RPA3401, Northeast Structural Genom... -

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Basic information

Entry
Database: PDB / ID: 2jtv
TitleSolution Structure of protein RPA3401, Northeast Structural Genomics Consortium Target RpT7, Ontario Center for Structural Proteomics Target RP3384
ComponentsProtein of Unknown Function
KeywordsSTRUCTURAL GENOMICS / Protein with unknown function RPA3401 / Northeast Structural Genomics Consortium / NESG / PSI-2 / Protein Structure Initiative
Function / homologyWinged 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 / Uncharacterized protein
Function and homology information
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodSOLUTION NMR / molecular dynamics
AuthorsIgnatchenko, A. / Gutmanas, A. / Lemak, A. / Yee, A. / Karra, M. / Srisailam, S. / Arrowsmith, C. / Northeast Structural Genomics Consortium (NESG)
Citation
Journal: TO BE PUBLISHED
Title: Solution Structure of protein RPA3401, Northeast Structural Genomics Consortium Target RpT7, Ontario Center for Structural Proteomics Target RP3384
Authors: Ignatchenko, A. / Gutmanas, A. / Lemak, A. / Yee, A. / Karra, M. / Srisailam, S. / Arrowsmith, C.
#1: Journal: J.Biomol.Nmr / Year: 2011
Title: A novel strategy for NMR resonance assignment and protein structure determination.
Authors: Lemak, A. / Gutmanas, A. / Chitayat, S. / Karra, M. / Fares, C. / Sunnerhagen, M. / Arrowsmith, C.H.
History
DepositionAug 7, 2007Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 9, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Jan 18, 2012Group: Database references
Revision 1.3May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_nmr_software.name / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein of Unknown Function


Theoretical massNumber of molelcules
Total (without water)7,3791
Polymers7,3791
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 Protein of Unknown Function


Mass: 7379.232 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris (phototrophic)
Strain: CGA009 / Plasmid: p15Tv lic / Production host: Escherichia coli (E. coli) / References: UniProt: Q6N4D8

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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
1313D HNCO
1413D HNCA
1513D CBCA(CO)NH
1613D 1H-15N NOESY
1713D 1H-13C NOESY
1823D (H)CCH-TOCSY
1923D (H)CCH-TOCSY
11014D(PR) HBHACBCA(CO)NH
11114D(PR) HCC(CO)NH TOCSY
11223D 1H-13C NOESY
11313D 1H-13C aromatic NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.6 mM [U-13C; U-15N] RHA3401, 300 mM NaCl, 10 mM [U-99% 2H] TRIS, 1 mM Benzamidine, 0.01 % NaN3, 95% H2O/5% D2O95% H2O/5% D2O
20.6 mM [U-13C; U-15N] RHA3401, 300 mM NaCl, 10 mM [U-99% 2H] TRIS, 1 mM Benzamidine, 0.01 % NaN3, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.6 mMRHA3401[U-13C; U-15N]1
300 mMNaCl1
10 mMTRIS[U-99% 2H]1
1 mMBenzamidine1
0.01 %NaN31
0.6 mMRHA3401[U-13C; U-15N]2
300 mMNaCl2
10 mMTRIS[U-99% 2H]2
1 mMBenzamidine2
0.01 %NaN32
Sample conditionsIonic strength: 300 / pH: 7.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE5001
Bruker AvanceBrukerAVANCE6002

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Processing

NMR software
NameDeveloperClassification
CNSBrunger, A.T. et al.structure solution
CNSBrunger, A.T. et al.refinement
NMRPipeDelaglio, F. et al.processing
TALOSCornilescu, G. et al.data analysis
SparkyGoddard, T.D. et al.data analysis
RefinementMethod: molecular dynamics / 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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