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- PDB-2k4n: NMR structure of protein PF0246 from Pyrococcus furiosus: target ... -

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Basic information

Entry
Database: PDB / ID: 2k4n
TitleNMR structure of protein PF0246 from Pyrococcus furiosus: target PfR75 from the Northeast Structural Genomics Consortium
ComponentsProtein PF0246
Keywordsstructural genomics / unknown function / beta-sheet / alpha-helix / mobile loop / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homologySignal recognition particle alu RNA binding heterodimer, srp9/1 - #70 / Protein of unknown function DUF5748 / Family of unknown function (DUF5748) / Signal recognition particle alu RNA binding heterodimer, srp9/1 / 2-Layer Sandwich / Alpha Beta / Uncharacterized protein
Function and homology information
Biological speciesPyrococcus furiosus (archaea)
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing
AuthorsCort, J.R. / Ho, C.K. / Shetty, K. / Cunningham, K. / Ma, L. / Xiao, R. / Liu, J. / Baran, M.C. / Swapna, G. / Acton, T.B. ...Cort, J.R. / Ho, C.K. / Shetty, K. / Cunningham, K. / Ma, L. / Xiao, R. / Liu, J. / Baran, M.C. / Swapna, G. / Acton, T.B. / Rost, B. / Montelione, G.T. / Kennedy, M.A. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution-State NMR Structure of protein PF0246 from Pyrococcus Furiosis
Authors: Cort, J.R.
History
DepositionJun 13, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 12, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 19, 2020Group: Data collection / Derived calculations / Other
Category: pdbx_database_status / pdbx_nmr_software ...pdbx_database_status / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name
Revision 1.3Jun 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 1.4May 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:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein PF0246


Theoretical massNumber of molelcules
Total (without water)13,4591
Polymers13,4591
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 30structures with lowest energy and fewest restraint violations
RepresentativeModel #1no criteria used

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Components

#1: Protein Protein PF0246


Mass: 13459.262 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Species: furiosus / Gene: PF0246 / Plasmid: pET21 / Species (production host): coli / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q8U449

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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 CBCA(CO)NH
1413D HN(CA)CB
1513D (H)CCH-TOCSY
1613D 1H-15N NOESY
1713D 1H-13C NOESY
1813D (H)CCH-COSY
1924D 13C-13C HMQC NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-100% 13C; U-100% 15N] PA0426, 95 % H2O, 5 % [U-100% 2H] D2O, 100 mM sodium chloride, 20 mM MES, 5 mM calcium chloride, 0.02 % sodium azide, 95% H2O/5% D2O95% H2O/5% D2O
21 mM [U-100% 13C; U-100% 15N] PA0426, 100 % [U-100% 2H] D2O, 100 mM sodium chloride, 20 mM MES, 5 mM calcium chloride, 0.02 % sodium azide, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMPA0426[U-100% 13C; U-100% 15N]1
95 %H2O1
5 %D2O[U-100% 2H]1
100 mMsodium chloride1
20 mMMES1
5 mMcalcium chloride1
0.02 %sodium azide1
1 mMPA0426[U-100% 13C; U-100% 15N]2
100 %D2O[U-100% 2H]2
100 mMsodium chloride2
20 mMMES2
5 mMcalcium chloride2
0.02 %sodium azide2
Sample conditionsIonic strength: 150 / pH: 6.5 / Pressure: ambient / Temperature: 313 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA7502

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Processing

NMR software
NameVersionDeveloperClassification
Felix98Accelrys Software Inc.processing
Felix98Accelrys Software Inc.data analysis
SparkyGoddarddata analysis
SparkyGoddardpeak picking
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
AutoStructureHuang, Tejero, Powers and Montelionestructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: torsion angle dynamics, simulated annealing / Software ordinal: 1
Details: initial structures generated with AutoStructure, Structures were refined with XPLOR-NIH and CNS
NMR representativeSelection criteria: no criteria used
NMR ensembleConformer selection criteria: structures with lowest energy and fewest restraint violations
Conformers calculated total number: 30 / Conformers submitted total number: 20

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