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- PDB-2kkm: Solution NMR structure of yeast protein YOR252W [residues 38-178]... -

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Basic information

Entry
Database: PDB / ID: 2kkm
TitleSolution NMR structure of yeast protein YOR252W [residues 38-178]: Northeast Structural Genomics Consortium target YT654
ComponentsTranslation machinery-associated protein 16
KeywordsTRANSLATION / translation machinery associated protein 16 / Nucleus / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homologyTranslation machinery-associated protein 16-like / Translation machinery-associated protein 16 / Tma16 superfamily / Translation machinery-associated protein 16 / de novo design (two linked rop proteins) / Up-down Bundle / Mainly Alpha / nucleus / Translation machinery-associated protein 16
Function and homology information
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / molecular dynamics, simulated annealing
Model detailsno criteria, model 1
AuthorsCort, J.R. / Yee, A. / Liu, C. / Arrowsmith, C.H. / Montelione, G.T. / Kennedy, M.A. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution NMR structure of yeast protein YOR252W
Authors: Cort, J.R. / Yee, A. / Liu, C. / Arrowsmith, C.H. / Montelione, G.T. / Kennedy, M.A.
History
DepositionJun 26, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 6, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 26, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
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: Translation machinery-associated protein 16


Theoretical massNumber of molelcules
Total (without water)16,9631
Polymers16,9631
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 40combination of lowest energy, fewest restraint violations, and favorable geometry
RepresentativeModel #1no criteria

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Components

#1: Protein Translation machinery-associated protein 16


Mass: 16963.271 Da / Num. of mol.: 1 / Fragment: sequence database residues 38-178
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: TMA16, YOR242W, YOR252W / Production host: Escherichia coli (E. coli) / References: UniProt: Q08687

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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 C(CO)NH
1513D HNCO
1613D HNCA
1713D HN(CA)CB
1813D HBHA(CO)NH
1913D H(CCO)NH
11013D (H)CCH-TOCSY
11113D HNHA
11213D HN(CO)CA
11313D 1H-15N NOESY
11413D 1H-13C NOESY
11524D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.6 mM [U-99% 13C; U-99% 15N] YOR252W, 300 mM sodium chloride, 10 mM DTT, 1 mM benzamidine, 0.01 % sodium azide, 93% H2O/7% D2O93% H2O/7% D2O
20.6 mM [U-99% 13C; U-99% 15N] YOR252W, 300 mM sodium chloride, 10 mM DTT, 1 mM benzamidine, 0.01 % sodium azide, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.6 mMYOR252W-1[U-99% 13C; U-99% 15N]1
300 mMsodium chloride-21
10 mMDTT-31
1 mMbenzamidine-41
0.01 %sodium azide-51
0.6 mMYOR252W-6[U-99% 13C; U-99% 15N]2
300 mMsodium chloride-72
10 mMDTT-82
1 mMbenzamidine-92
0.01 %sodium azide-102
Sample conditionsIonic strength: 300 / pH: 7 / Pressure: ambient / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA7501
Varian INOVAVarianINOVA8002
Varian INOVAVarianINOVA6003

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Processing

NMR software
NameDeveloperClassification
AutoStructureHuang, Tejero, Powers and Montelionestructure solution
AutoStructureHuang, Tejero, Powers and Montelionerefinement
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
PSVSBhattacharya and Montelionerefinement
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: molecular dynamics, simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: no criteria
NMR ensembleConformer selection criteria: combination of lowest energy, fewest restraint violations, and favorable geometry
Conformers calculated total number: 40 / Conformers submitted total number: 20

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