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- PDB-2akk: Solution structure of phnA-like protein rp4479 from Rhodopseudomo... -

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Basic information

Entry
Database: PDB / ID: 2akk
TitleSolution structure of phnA-like protein rp4479 from Rhodopseudomonas palustris
ComponentsphnA-like protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / beta-strand protein / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / Ontario Centre for Structural Proteomics / OCSP
Function / homologyProtein YjdM / Protein YjdM, C-terminal / PhnA domain / SH3 Domains / SH3 type barrels. / Roll / Mainly Beta / PhnA-like protein
Function and homology information
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodSOLUTION NMR / simulated annealing
AuthorsWu, B. / Yee, A. / Ramelot, T.A. / Semesi, A. / Lemak, A. / Kennedy, M. / Edward, A. / Arrowsmith, C.H. / Northeast Structural Genomics Consortium (NESG) / Ontario Centre for Structural Proteomics (OCSP)
CitationJournal: To be Published
Title: Solution structure of phnA-like protein rp4479 from Rhodopseudomonas palustris
Authors: Wu, B. / Yee, A. / Ramelot, T.A. / Semesi, A. / Lemak, A. / Kennedy, M. / Edward, A. / Arrowsmith, C.H.
History
DepositionAug 3, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 22, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Feb 5, 2020Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
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
Revision 1.5May 8, 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: phnA-like protein


Theoretical massNumber of molelcules
Total (without water)8,0911
Polymers8,0911
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
Representative

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Components

#1: Protein phnA-like protein / rp4479


Mass: 8091.396 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris (phototrophic)
Strain: CGA009 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6N1A7

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY
1314D 13C-separated NOESY

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Sample preparation

DetailsContents: 1mM rp4479, U-15N,13C: 450 mM NaCl, 25 mM Na2PO4, 1mM Benzamidine, 1xinhibitor cooktail, 0.01% NAN3, 95% H2O, 5% D2O
Solvent system: 95% H2O/5% D2O
Sample conditionsIonic strength: 450 mM NaCl, 25 mM Phosphate buffer / pH: 6.5 / Pressure: ambinet / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA8002

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2.3Delaglio, F.processing
CYANA2.1Gunter, P.structure solution
CNS1Brunger, A.T. et alrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: 1500 NOE-derived distance restraints and 75 torsion angle restraints
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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