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- PDB-2kds: Structure of Ribosomal Protein L14e from Sulfolobus solfataricus -

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Basic information

Entry
Database: PDB / ID: 2kds
TitleStructure of Ribosomal Protein L14e from Sulfolobus solfataricus
Components50S ribosomal protein L14e
KeywordsRIBOSOMAL PROTEIN / protein / hyperthmophile / sh3 / Ribonucleoprotein
Function / homology
Function and homology information


ribosomal large subunit biogenesis / cytosolic large ribosomal subunit / structural constituent of ribosome / translation / RNA binding
Similarity search - Function
Ribosomal protein L14e / SH3 type barrels. - #30 / Ribosomal protein L14 / Ribosomal protein L14, KOW motif / SH3 type barrels. / Translation protein SH3-like domain superfamily / Ribosomal protein L2, domain 2 / Roll / Mainly Beta
Similarity search - Domain/homology
Large ribosomal subunit protein eL14
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodSOLUTION NMR / simulated annealing
Model detailsclosest to the average, model 1
AuthorsEdmondson, S.P. / Shriver, J.W.
CitationJournal: To be Published
Title: Structure and Stability of the Archael L14e Ribosomal Protein from Sulfolobus solfataricus
Authors: Edmondson, S.P. / Clark, A.T. / Turri, J.S. / Smith, K.L. / Shriver, J.W.
History
DepositionJan 15, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 12, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 24, 2012Group: Structure summary

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 50S ribosomal protein L14e


Theoretical massNumber of molelcules
Total (without water)10,7511
Polymers10,7511
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)10 / 100target function
RepresentativeModel #1closest to the average

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Components

#1: Protein 50S ribosomal protein L14e


Mass: 10750.688 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Strain: P2 / Gene: rpl14e, SSO5763 / Plasmid: pETBlue-2 / Production host: Escherichia coli (E. coli) / Strain (production host): RosettaBlue(DE3) / References: UniProt: Q980C1

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1132D 1H-15N HSQC
1213D HNCO
1313D HN(CA)CB
1413D CBCA(CO)NH
1513D HNCA
1613D HN(CO)CA
1713D HNHA
1813D HCC TOCSY-NNH
1913D CCC-TOCSY-NNH
11023D (H)CCH-TOCSY
11123D (H)CCH-COSY
1121(HB)CB(CGCD)HD
11312D DQF-COSY
11412D 1H-1H NOESY
11512D 1H-13C HSQC
11613D 1H-15N NOESY
11723D 1H-13C NOESY
11822D 1H-15N HSQC
11912D 1H-15N NOE
12012D 1H-15N T1
12112D 1H-15N T1rho
12243D HNCO-IPAP

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-100% 13C; U-100% 15N] L14e ribosomal protein-1, 90% H2O/10% D2O90% H2O/10% D2O
21 mM [U-100% 13C; U-100% 15N] L14e ribosomal protein-2, 100% D2O100% D2O
31 mM [U-100% 15N] L14e ribosomal protein-3, 0.2 mM DSS-4, 90% H2O/10% D2O90% H2O/10% D2O
41 mM [U-100% 15N] L14e ribosomal protein-5, 5 % C12E5-6, 1.0 r hexanol-7, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mML14e ribosomal protein-1[U-100% 13C; U-100% 15N]1
1 mML14e ribosomal protein-2[U-100% 13C; U-100% 15N]2
1 mML14e ribosomal protein-3[U-100% 15N]3
0.2 mMDSS-43
1 mML14e ribosomal protein-5[U-100% 15N]4
5 %C12E5-64
1.0 %hexanol-74
Sample conditionsIonic strength: 0 / pH: 5.0 / Pressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA8001
Varian INOVAVarianINOVA5002

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Processing

NMR software
NameVersionDeveloperClassification
VNMRVariancollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewaquaJohnson, One Moon Scientificpeak picking
NMRViewaquaJohnson, One Moon Scientificchemical shift assignment
ARIA1.2Linge, O'Donoghue and Nilgeschemical shift assignment
X-PLOR_NIH2.19Schwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 1307 / NOE intraresidue total count: 584 / NOE long range total count: 246 / NOE medium range total count: 192 / NOE sequential total count: 285 / Hydrogen bond constraints total count: 58 / Protein phi angle constraints total count: 42 / Protein psi angle constraints total count: 42
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 10
NMR ensemble rmsDistance rms dev: 0.048 Å

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