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- PDB-2kcp: SOLUTION STRUCTURE OF 30S RIBOSOMAL PROTEIN S8E; FROM Methanother... -

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Basic information

Entry
Database: PDB / ID: 2kcp
TitleSOLUTION STRUCTURE OF 30S RIBOSOMAL PROTEIN S8E; FROM Methanothermobacter thermautotrophicus, NORTHEASTSTRUCTURAL GENOMICS CONSORTIUM (NESG) TARGET Tr71d
Components30S ribosomal protein S8e
KeywordsRIBOSOMAL PROTEIN / rps8e / 30S ribosomal protein S8e / beta / nesg / Ribonucleoprotein / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homology
Function and homology information


maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / cytosolic small ribosomal subunit / structural constituent of ribosome / translation
Similarity search - Function
Thrombin, subunit H - #310 / Ribosomal protein S8e, archaeal / Ribosomal protein S8e, conserved site / Ribosomal protein S8e signature. / Ribosomal protein S8e / Ribosomal protein S8e/ribosomal biogenesis NSA2 / Ribosomal protein S8e / Thrombin, subunit H / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Small ribosomal subunit protein eS8
Similarity search - Component
Biological speciesMethanothermobacter thermautotrophicus str. Delta H (archaea)
MethodSOLUTION NMR / distance geometry, simulated annealing, molecular dynamics, torsion angle dynamics
Model detailslowest energy, model 1
AuthorsLiu, G. / Rossi, P. / Wang, D. / Nwosu, C. / Owens, L. / Xiao, R. / Liu, J. / Baran, M.C. / Swapna, G. / Acton, T.B. ...Liu, G. / Rossi, P. / Wang, D. / Nwosu, C. / Owens, L. / Xiao, R. / Liu, J. / Baran, M.C. / Swapna, G. / Acton, T.B. / Rost, B. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: SOLUTION STRUCTURE OF 30S RIBOSOMAL PROTEIN S8E FROM Methanothermobacter thermautotrophicus, NORTHEASTSTRUCTURAL GENOMICS CONSORTIUM (NESG) TARGET
Authors: Liu, G. / Montelione, G.T.
History
DepositionDec 24, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 14, 2009Provider: 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_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
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: 30S ribosomal protein S8e


Theoretical massNumber of molelcules
Total (without water)11,0411
Polymers11,0411
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 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein 30S ribosomal protein S8e


Mass: 11041.483 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermobacter thermautotrophicus str. Delta H (archaea)
Gene: rps8e, MTH_207 / Plasmid: pET 21-23C / Production host: Escherichia coli (E. coli) / References: UniProt: O26309

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: Residues 1-20 residues and 44-57 are flexible and not defined.
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-15N HSQC
1312D 1H-15N HSQC
1422D 1H-15N HSQC
1513D 1H-15N NOESY
1613D 1H-13C NOESY
1733D 1H-13C NOESY
1813D CBCA(CO)NH
1913D HN(CA)CB
11013D HBHA(CO)NH
11113D (H)CCH-TOCSY
11232D 1H-13C HSQC
11322D 1H-13C HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
10.94 mM [U-100% 13C; U-100% 15N] rps8e-1, 95% H2O/5% D2O95% H2O/5% D2O
21 mM [U-10% 13C; U-100% 15N] rps8e-2, 95% H2O/5% D2O95% H2O/5% D2O
30.94 mM [U-100% 13C; U-100% 15N] rps8e-3, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.94 mMrps8e-1[U-100% 13C; U-100% 15N]1
1 mMrps8e-2[U-10% 13C; U-100% 15N]2
0.94 mMrps8e-3[U-100% 13C; U-100% 15N]3
Sample conditionsIonic strength: n.a. / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker AvanceBrukerAVANCE8002
Varian INOVAVarianINOVA6003

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Processing

NMR software
NameDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
CYANAGuntert, Mumenthaler and Wuthrichrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CYANAGuntert, Mumenthaler and Wuthrichgeometry optimization
AutoStructureHuang, Tejero, Powers and Montelionepeak picking
AutoStructureHuang, Tejero, Powers and Montelionerefinement
AutoStructureHuang, Tejero, Powers and Montelionegeometry optimization
PSVSBhattacharya and Montelionegeometry optimization
AutoAssignZimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
XEASYBartels et al.chemical shift assignment
XEASYBartels et al.data analysis
XEASYBartels et al.peak picking
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TopSpinBruker Biospincollection
VnmrJVariancollection
RefinementMethod: distance geometry, simulated annealing, molecular dynamics, torsion angle dynamics
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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