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- PDB-2lp6: Refined Solution NMR Structure of the 50S ribosomal protein L35Ae... -

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Basic information

Entry
Database: PDB / ID: 2lp6
TitleRefined Solution NMR Structure of the 50S ribosomal protein L35Ae from Pyrococcus furiosus, Northeast Structural Genomics Consortium Target (NESG) PfR48
Components50S ribosomal protein L35Ae
KeywordsRIBOSOMAL PROTEIN / Structural Genomics / NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG) / PSI-Biology / 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
Model detailslowest energy, model 1
AuthorsSnyder, D.A. / Aramini, J.M. / Yu, B. / Huang, Y.J. / Xiao, R. / Cort, J.R. / Shastry, R. / Ma, L. / Liu, J. / Rost, B. ...Snyder, D.A. / Aramini, J.M. / Yu, B. / Huang, Y.J. / Xiao, R. / Cort, J.R. / Shastry, R. / Ma, L. / Liu, J. / Rost, B. / Acton, T.B. / Kennedy, M.A. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: Proteins / Year: 2012
Title: Solution NMR structure of the ribosomal protein RP-L35Ae from Pyrococcus furiosus.
Authors: Snyder, D.A. / Aramini, J.M. / Yu, B. / 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
DepositionFeb 2, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 15, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 11, 2012Group: Database references
Revision 1.2Jun 20, 2012Group: Database references
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / 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_status.status_code_nmr_data / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.4May 15, 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: 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)20 / 100structures 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) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / Gene: PF1872, rpl35Ae / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pMgK / References: UniProt: Q8TZV6

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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 aliphatic
1312D 1H-13C HSQC aromatic
1413D HNCO
1513D CBCA(CO)NH
1613D HN(CA)CB
1713D HBHA(CO)NH
1813D CCC(CO)NH TOCSY
1913D (H)CCH-TOCSY
11013D (H)CCH-COSY
11113D HNHA
11213D 1H-15N NOESY
11323D 1H-13C NOESY aliphatic
11413D 1H-13C NOESY aromatic
11513D 1H-13C NOESY aliphatic
11632D 1H-13C HSQC high resolution
NMR detailsText: THE PROTEIN IS MONOMERIC BY GEL FILTRATION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING AND 15N T1/T2 RELAXATION. THE STRUCTURE WAS DETERMINED USING TRIPLE RESONANCE NMR SPECTROSCOPY. AUTOMATIC ...Text: THE PROTEIN IS MONOMERIC BY GEL FILTRATION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING AND 15N T1/T2 RELAXATION. THE STRUCTURE WAS DETERMINED USING TRIPLE RESONANCE NMR SPECTROSCOPY. AUTOMATIC BACKBONE RESONANCE ASSIGNMENTS WERE MADE USING AUTOASSIGN, FOLLOWED BY MANUAL SIDE CHAIN ASSIGNMENT. AUTOMATIC NOESY ASSIGNMENTS WERE DETERMINED USING CYANA 3.0. BACKBONE (PHI/PSI) DIHEDRAL ANGLE CONSTRAINTS WERE OBTAINED FROM TALOSplus, AND HYDROGEN BOND CONSTRAINTS WERE DETERMINED USING AUTOSTRUCTURE. COMPLETENESS OF NMR ASSIGNMENTS (EXCLUDING THE C-TERMINAL HIS6): BACKBONE, 98.2%, SIDE CHAIN, 90.9%, AROMATICS, 100%, STEREOSPECIFIC METHYL, 84.2%. FINAL STRUCTURE QUALITY FACTORS (FOR RESIDUES 1 TO 91, PSVS 1.4), WHERE ORDERED RESIDUES [S(PHI) + S(PSI) > 1.8] COMPRISE: 2-12,21-76,79-87: (A) RMSD (ORDERED RESIDUES): BB, 0.5, HEAVY ATOM, 1.0. (B) MOLPROBITY RAMACHANDRAN STATISTICS FOR ORDERED RESIDUES: MOST FAVORED, 97.0%, ADDITIONALLY ALLOWED, 3.0%, DISALLOWED, 0%. (C) PROCHECK SCORES FOR ORDERED RESIDUES (RAW/Z-): PHI-PSI, -0.56/-1.89, ALL, -0.26/-1.54. (D) MOLPROBITY CLASH SCORE (RAW/Z-): 15.13/-1.07 (E) RPF SCORES FOR GOODNESS OF FIT TO NOESY DATA (RESIDUES 1 TO 91): RECALL, 0.965, PRECISION, 0.878, F-MEASURE, 0.920, DP-SCORE, 0.784. (F) NUMBER OF CLOSE CONTACTS PER 20 MODELS: 5. THE FINAL FOUR UNASSIGNED HISTIDINE RESIDUES IN THE C-TERMINAL AFFINITY TAG WERE NOT INCLUDED IN THE STRUCTURE CALCULATIONS AND HAVE BEEN OMITTED FROM THIS DEPOSITION. COORDINATES FOR THE FOLLOWING RESIDUES ARE NOT WELL DETERMINED [S(PHI) + S(PSI) < 1.8]: 1,13-20,77-78,88-91.

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Sample preparation

Details
Solution-IDContentsSolvent system
11.07 mM [U-100% 13C; U-100% 15N] PfR48.005, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 100 mM NaCL, 1 x Proteinase Inhibitors, 20 mM MES pH 6.5, 50 uM DSS, 90% H2O/10% D2O90% H2O/10% D2O
21.07 mM [U-100% 13C; U-100% 15N] PfR48.005, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 100 mM NaCL, 1 x Proteinase Inhibitors, 20 mM MES pH 6.5, 50 uM DSS, 100% D2O100% D2O
30.29 mM [U-5% 13C; U-100% 15N] PfR48.002, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 100 mM NaCL, 1 x Proteinase Inhibitors, 20 mM MES pH 6.5, 50 uM DSS, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.07 mMPfR48.005-1[U-100% 13C; U-100% 15N]1
0.02 %NaN3-21
10 mMDTT-31
5 mMCaCL2-41
100 mMNaCL-51
1 %Proteinase Inhibitors-61
20 mMMES pH 6.5-71
50 uMDSS-81
1.07 mMPfR48.005-9[U-100% 13C; U-100% 15N]2
0.02 %NaN3-102
10 mMDTT-112
5 mMCaCL2-122
100 mMNaCL-132
1 %Proteinase Inhibitors-142
20 mMMES pH 6.5-152
50 uMDSS-162
0.29 mMPfR48.002-17[U-5% 13C; U-100% 15N]3
0.02 %NaN3-183
10 mMDTT-193
5 mMCaCL2-203
100 mMNaCL-213
1 %Proteinase Inhibitors-223
20 mMMES pH 6.5-233
50 uMDSS-243
Sample conditionspH: 6.5 / Pressure: ambient / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA7502
Varian INOVAVarianINOVA8003

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.3Brunger, Adams, Clore, Gros, Nilges and Readrefinement
CNS1.3Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNS1.3Brunger, Adams, Clore, Gros, Nilges and Readgeometry optimization
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
AutoStructure2.2.1Huang, Tejero, Powers and Montelionedata analysis
AutoAssign1.9Zimmerman, Moseley, Kulikowski and Montelionedata analysis
AutoAssign1.9Zimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
NMRPipe2.3Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
VNMR6.1BVariancollection
Sparky3Goddarddata analysis
TALOS+Shen, Cornilescu, Delaglio and Baxstructure solution
PSVS1.4Bhattacharya, Montelionedata analysis
PdbStat5.5Tejero, Montelionedata analysis
MolProbity3.19Richardsondata analysis
RefinementMethod: simulated annealing / Software ordinal: 1
Details: THE FINAL REFINED STRUCTURES ARE BASED ON A TOTAL OF 1402 CONFORMATIONALLY-RESTRICTING NOE-DERIVED DISTANCE CONSTRAINTS, 153 DIHEDRAL ANGLE CONSTRAINTS, AND 56 HYDROGEN BOND CONSTRAINTS (18. ...Details: THE FINAL REFINED STRUCTURES ARE BASED ON A TOTAL OF 1402 CONFORMATIONALLY-RESTRICTING NOE-DERIVED DISTANCE CONSTRAINTS, 153 DIHEDRAL ANGLE CONSTRAINTS, AND 56 HYDROGEN BOND CONSTRAINTS (18.3 CONSTRAINTS PER RESIDUE, 7.0 LONG RANGE CONSTRAINTS PER RESIDUE, COMPUTED FOR RESIDUES 1 TO 91 BY PSVS 1.4). STRUCTURE DETERMINATION WAS PERFORMED ITERATIVELY USING CYANA 3.0. THE 20 STRUCTURES OUT OF 100 WITH THE LOWEST TARGET FUNCTION WERE FURTHER REFINED BY RESTRAINED MOLECULAR DYNAMICS/ENERGY MINIMIZATION IN EXPLICIT WATER (CNS 1.3) WITH PARAM19.
NMR constraintsNOE constraints total: 1402
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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