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- PDB-1sqr: Solution Structure of the 50S Ribosomal Protein L35AE from Pyroco... -

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Basic information

Entry
Database: PDB / ID: 1sqr
TitleSolution Structure of the 50S Ribosomal Protein L35AE from Pyrococcus furiosus. Northeast Structural Genomics Consortium Target PfR48.
Components50S ribosomal protein L35Ae
KeywordsRIBOSOME / PfR48 / AUTOSTRUCTURE / RIBOSOMAL PROTEIN / NORTHEAST STRUCTURAL GENOMICS CONSORTIUM / BETA-BARREL / NESG / STRUCTURAL GENOMICS / PSI / PROTEIN STRUCTURE INITIATIVE
Function / homology
Function and homology information


ribosomal large subunit biogenesis / cytosolic large ribosomal subunit / cytoplasmic translation / structural constituent of ribosome
Similarity search - Function
translation elongation factor selb, chain A, domain 4 / Ribosomal protein L35Ae, conserved site / Ribosomal protein L35Ae signature. / Ribosomal protein L35A / Ribosomal protein L35Ae / Ribosomal protein L35A superfamily / Thrombin, subunit H / Translation protein, beta-barrel domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Large ribosomal subunit protein eL33
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodSOLUTION NMR / simulated annealing
AuthorsSnyder, D.A. / Aramini, J.M. / Huang, Y.J. / Xiao, R. / Cort, J.R. / Shastry, R. / Ma, L.C. / Liu, J. / Rost, B. / Acton, T.B. ...Snyder, D.A. / Aramini, J.M. / Huang, Y.J. / Xiao, R. / Cort, J.R. / Shastry, R. / Ma, L.C. / Liu, J. / Rost, B. / Acton, T.B. / Kennedy, M.A. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution Structure of the 50S Ribosomal Protein L35AE from Pyrococcus furiosus: Northeast Structural Genomics Consortium Target PfR48
Authors: Snyder, D.A. / Aramini, J.M. / Huang, Y.J. / Xiao, R. / Cort, J.R. / Shastry, R. / Ma, L.C. / Liu, J. / Rost, B. / Acton, T.B. / Kennedy, M.A. / Montelione, G.T.
History
DepositionMar 19, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 16, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_database_related ...database_2 / pdbx_database_related / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_related.db_name / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 50S ribosomal protein L35Ae


Theoretical massNumber of molelcules
Total (without water)10,8271
Polymers10,8271
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 / 56structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein 50S ribosomal protein L35Ae


Mass: 10826.713 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Gene: RPL35AE, PF1872 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)MGK / References: UniProt: Q8TZV6

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-NOESY (aliphatic), (H)CCH-COSY
1223D 13C-NOESY (aliphatic and aromatic), 13C,1H-HSQC
1324D 13C-separated NOESY
1413D-TOCSYs
154H/D EXCHANGE
1633D 15N-NOESY, backbone TR experiments
171high-resolution/non-constant-time 13C,1H-HSQC
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY. AUTOMATIC BACKBONE RESONANCE ASSIGNMENTS WERE MADE USING AUTOASSIGN. MANUAL SIDE CHAIN ASSIGNMENTS. AUTOMATIC NOESY ...Text: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY. AUTOMATIC BACKBONE RESONANCE ASSIGNMENTS WERE MADE USING AUTOASSIGN. MANUAL SIDE CHAIN ASSIGNMENTS. AUTOMATIC NOESY ASSIGNMENTS AS WELL AS DISTANCE AND HYDROGEN BOND RESTRAINTS WERE DETERMINED USING AUTOSTRUCTURE. DIHEDRAL ANGLE RESTRAINTS WERE DETERMINED USING HYPER AND TALOS. BACKBONE DIHEDRAL ANGLES FOR RESIDUES 1, 13-20, 26-27, 39-40, 47-51, 54, 63-66 AND 73-79 ARE NOT WELL-DEFINED [S(PHI) + S(PSI) < 1.8] IN THIS SOLUTION NMR STRUCTURE.

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Sample preparation

Details
Solution-IDContentsSolvent system
11.07 MM PfR48 U-15N,13C 20 MM MES, 100 MM NACL, 5 MM CACL2, 10 MM DTT, 0.02% NAN3, PH 6.595% H2O/5% D2O
21.07 MM PfR48 U-15N,13C 20 MM MES, 100 MM NACL, 5 MM CACL2, 10 MM DTT, 0.02% NAN3, PH 6.5100% D2O
30.1 MM PfR48 U-15N,5%-13C 20 MM MES, 100 MM NACL, 5 MM CACL2, 10 MM DTT, 0.02% NAN3, PH 6.595% H2O/5% D2O
40.5 MM PfR48 U-15N 20 MM MES, 100 MM NACL, 5 MM CACL2, 10 MM DTT, 0.02% NAN3, PH 6.595% H2O/5% D2O
Sample conditionsIonic strength: 100 mM / pH: 6.5 / Pressure: ambient / Temperature: 293 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA8001
Varian INOVAVarianINOVA7502
Varian INOVAVarianINOVA6003
Varian UNITYVarianUNITY6004

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Processing

NMR software
NameVersionDeveloperClassification
X-PLORNIH 2.0.6Schwieters, et al.refinement
VNMR6.1BVariancollection
NMRPipe2.1Delaglio, et al.processing
Sparky3.106Goddarddata analysis
PdbStat3.32Tejero and Montelionestructure solution
AutoStructure2.0.0Huang and Montelionerefinement
HYPER3.2Tejero and Montelionestructure solution
AutoAssign1.9Zimmerman, Moseley and Montelionedata analysis
TALOS2.1Cornilescu, Delaglio and Baxstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
Details: THE STRUCTURES ARE BASED ON A TOTAL OF 1157 CONFORMATIONALLY-RESTRICTING NOE-DERIVED DISTANCE RESTRAINTS, 177 DIHEDRAL ANGLE RESTRAINTS, AND 32 HYDROGEN BOND RESTRAINTS. (14.4 CONSTRAINTS ...Details: THE STRUCTURES ARE BASED ON A TOTAL OF 1157 CONFORMATIONALLY-RESTRICTING NOE-DERIVED DISTANCE RESTRAINTS, 177 DIHEDRAL ANGLE RESTRAINTS, AND 32 HYDROGEN BOND RESTRAINTS. (14.4 CONSTRAINTS PER RESIDUE; 6.1 LONG-RANGE RESTRAINTS PER RESIDUE). STRUCTURE DETERMINATION WAS PERFORMED ITERATIVELY USING AUTOSTRUCTURE (XPLOR). THE UNSTRUCTURED 8 RESIDUE C-TERMINAL TAG (LEHHHHHH) WAS INCLUDED IN THE STRUCTURE CALCULATIONS BUT IS OMITTED FROM THIS DEPOSITION.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 56 / Conformers submitted total number: 10

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