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- PDB-1qkh: SOLUTION STRUCTURE OF THE RIBOSOMAL PROTEIN S19 FROM THERMUS THER... -

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Basic information

Entry
Database: PDB / ID: 1qkh
TitleSOLUTION STRUCTURE OF THE RIBOSOMAL PROTEIN S19 FROM THERMUS THERMOPHILUS
Components30S RIBOSOMAL PROTEIN S19
KeywordsRIBOSOMAL PROTEIN / RIBOSOME / THERMUS THERMOPHILUS / S19
Function / homology
Function and homology information


small ribosomal subunit / rRNA binding / structural constituent of ribosome / translation / cytoplasm
Similarity search - Function
30s Ribosomal Protein S19; Chain A / Ribosomal protein S19/S15 / Ribosomal protein S19, bacterial-type / Ribosomal protein S15/S19, conserved site / Ribosomal protein S19 signature. / Ribosomal protein S19/S15 / Ribosomal protein S19/S15, superfamily / Ribosomal protein S19 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Small ribosomal subunit protein uS19
Similarity search - Component
Biological speciesTHERMUS THERMOPHILUS (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsHelgstrand, M. / Rak, A.V. / Allard, P. / Davydova, N. / Garber, M.B. / Hard, T.
CitationJournal: J. Mol. Biol. / Year: 1999
Title: Solution structure of the ribosomal protein S19 from Thermus thermophilus.
Authors: Helgstrand, M. / Rak, A.V. / Allard, P. / Davydova, N. / Garber, M.B. / Hard, T.
History
DepositionJul 20, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 21, 1999Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 17, 2018Group: Database references / Category: citation / pdbx_database_related
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _pdbx_database_related.details
Remark 650 HELIX DETERMINATION METHOD: KABSCH AND SANDER
Remark 700 SHEET DETERMINATION METHOD: KABSCH AND SANDER

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 30S RIBOSOMAL PROTEIN S19


Theoretical massNumber of molelcules
Total (without water)10,4741
Polymers10,4741
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)21 / 50CUMULATIVE RMSD OF STRUCTURES SORTED AFTER TOTAL ENERGY
Representative

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Components

#1: Protein 30S RIBOSOMAL PROTEIN S19 /


Mass: 10474.269 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMUS THERMOPHILUS (bacteria) / Plasmid: PTTHS19 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834(DE3) / References: UniProt: P80381

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111HNCA
121HN(CO)CA
131CBCANH
141CBCA(CO)NH
151C(CO)NH-TOCSY
161(H)CCH-TOCSY
171(HB)CB(CGCD)HD
181(HB)CB(CGCDCE)HE
19115N-EDITED NOESY-HSQC
110115N-EDITED TOCSY-HSQC
11113D HNHA
11212D NOESY
11312D TOCSY

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Sample preparation

DetailsContents: 90% WATER/10% D2O
Sample conditionsIonic strength: 0.250 M / pH: 6.5 / Pressure: 1 atm / Temperature: 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA5001
Varian INOVAVarianINOVA6002
Varian INOVAVarianINOVA8003

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.851BRUNGER STRUCTURAL STATISTICS: 21 SA STRUCTURES SAAVEMIN[A] RMS DEVIATIONS FROM EXP. RESTRAINTS NOE DISTANCE RESTRAINTS (1104) 0.036 A 0.032 A DIHEDRAL ANGLE RESTRAINTS (42) 0.380 DEG 0.380 DEG DEVIATIONS FROM IDEAL GEOMETRY BONDS 0.0045 A 0.0041 A ANGLES 0.71 DEG 0.66 DEG IMPROPERS 0.54 DEG 0.49 DEGrefinement
VNMR5.3structure solution
PRONTO (VERSION 970523)970523)structure solution
X-PLOR (VERSION 3.851)3.851)structure solution
MOLMOL (VERSION 2.6)2.6)structure solution
PROCHECK-NMRstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
Details: THE STRUCTURE WAS DETERMINED USING 1104 DISTANCE RESTRAINTS, 42 DIHEDRAL ANGLE RESTRAINTS AND 14 HYDROGEN BOND RESTRAINTS. 50 STRUCTURES WERE CALCULATED AND REFINED USING AN AB INITIO ...Details: THE STRUCTURE WAS DETERMINED USING 1104 DISTANCE RESTRAINTS, 42 DIHEDRAL ANGLE RESTRAINTS AND 14 HYDROGEN BOND RESTRAINTS. 50 STRUCTURES WERE CALCULATED AND REFINED USING AN AB INITIO SIMULATED ANNEALING PROTOCOL FOR X- PLOR AND THEN REFINED IN TWO STEPS. AN R-6 AVERAGING PROTOCOL WAS USED FOR NON-STEREOSPECIFICALLY ASSIGNED PROTONS [1]. DURING THE SIMULATED ANNEALING STEP AND THE FIRST REFINEMENT STEP ONLY THE REPULSIVE PART OF THE VAN DER WAALS INTERACTION WAS INCLUDED. IN THE SECOND REFINEMENT STEP THE VAN DER WAALS INTERACTION WAS PARAMETERIZED USING A LENNARD-JONES POTENTIAL INCLUDING THE ATTRACTIVE PART. 21 STRUCTURES WERE SELECTED ON THE BASIS OF CUMULATIVE RMSD VALUES OF STRUCTURES, ORDERED AFTER OVERALL ENERGY, AND RAMACHANDRAN BEHAVIOR FOR REGIONS WITH LOW RESTRAINT DENSITIES. [1] BRUNGER, A. T., CLORE, G. M., GRONENBORN, A. M. & KARPLUS, M. (1986). THREE-DIMENSIONAL STRUCTURE OF PROTEINS DETERMINED BY MOLECULAR DYNAMICS WITH INTERPROTON DISTANCE RESTRAINTS: APPLICATION TO CRAMBIN. PROC NATL ACAD SCI USA 83, 3801-3805. OTHER DETAILS OF STRUCTURE REFINEMENT CAN BE FOUND IN THE JRNL CITATION.
NMR ensembleConformer selection criteria: CUMULATIVE RMSD OF STRUCTURES SORTED AFTER TOTAL ENERGY
Conformers calculated total number: 50 / Conformers submitted total number: 21

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