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- PDB-2kku: Solution structure of protein af2351 from Archaeoglobus fulgidus.... -

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Basic information

Entry
Database: PDB / ID: 2kku
TitleSolution structure of protein af2351 from Archaeoglobus fulgidus. Northeast Structural Genomics Consortium target AtT9/Ontario Center for Structural Proteomics Target af2351
ComponentsUncharacterized protein
KeywordsStructural Genomics / Unknown function / alpha/beta protein / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / Ontario Centre for Structural Proteomics / OCSP
Function / homologyProtein of unknown function DUF365 / Domain of unknown function (DUF365) / Hypothetical protein. / Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 / Roll / Mainly Beta / Uncharacterized protein
Function and homology information
Biological speciesArchaeoglobus fulgidus (archaea)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsWu, B. / Yee, A. / Fares, C. / Lemak, A. / Rumpel, S. / Semest, A. / Montelione, G.T. / Arrowsmith, C.H. / Northeast Structural Genomics Consortium (NESG) / Ontario Centre for Structural Proteomics (OCSP)
Citation
Journal: To be Published
Title: Solution structure of protein af2351 from Archaeoglobus fulgidus. Northeast Structural Genomics Consortium target AtT9/Ontario Center for Structural Proteomics Target af2351
Authors: Wu, B. / Yee, A. / Fares, C. / Lemak, A. / Rumpel, S. / Semest, A. / Montelione, G.T. / Arrowsmith, C.H.
#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
DepositionJun 29, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 14, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 18, 2012Group: Database references
Revision 1.3Feb 26, 2020Group: Data collection / Database references / Other
Category: pdbx_database_status / pdbx_nmr_software ...pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name ..._pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _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:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)19,2631
Polymers19,2631
Non-polymers00
Water0
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: 19263.461 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Gene: AF_2351 / Production host: Escherichia coli (E. coli) / References: UniProt: O30319

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D HNCO
1213D CBCA(CO)NH
1313D HBHA(CO)NH
1413D HNCA
1513D (H)CCH-TOCSY
1613D CCH-TOCSY
1713D 1H-15N NOESY
1813D 1H-13C NOESY
1913D 1H-13C NOESY aromatic
11023D 1H-13C NOESY
11132D 1H-13C HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM [U-100% 13C; U-100% 15N] af2351, 25 mM bis-tris, 50 mM sodium chloride, 0.01 % sodium azide, 1 mM benzamidine, 90% H2O/10% D2O90% H2O/10% D2O
20.5 mM [U-100% 13C; U-100% 15N] af2351, 25 mM bis-tris, 50 mM sodium chloride, 0.01 % sodium azide, 1 mM benzamidine, 99.9% D2O99.9% D2O
30.5 mM [U-7% 13C; U-99% 15N] af2351, 25 mM bis-tris, 50 mM sodium chloride, 0.01 % sodium azide, 1 mM benzamidine, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMaf2351-1[U-100% 13C; U-100% 15N]1
25 mMbis-tris-21
50 mMsodium chloride-31
0.01 %sodium azide-41
1 mMbenzamidine-51
0.5 mMaf2351-6[U-100% 13C; U-100% 15N]2
25 mMbis-tris-72
50 mMsodium chloride-82
0.01 %sodium azide-92
1 mMbenzamidine-102
0.5 mMaf2351-11[U-7% 13C; U-99% 15N]3
25 mMbis-tris-123
50 mMsodium chloride-133
0.01 %sodium azide-143
1 mMbenzamidine-153
Sample conditionsIonic strength: 50 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE8002

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2.3Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
MDDGUI1Gutmanas and Arrowsmithprocessing
Sparky3.95Goddarddata analysis
Sparky3.95Goddardpeak picking
FAWN1Lemak and Arrowsmithchemical shift assignment
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
AutoStructureHuang, Tejero, Powers and Montelionenmr structure quality assessment
PSVSBhattacharya and Montelionenmr structure quality assessment
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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