[English] 日本語
Yorodumi
- PDB-1qkf: SOLUTION STRUCTURE OF THE RIBOSOMAL PROTEIN S19 FROM THERMUS THER... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1qkf
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


ribosomal small subunit assembly / 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
Model type detailsMINIMIZED AVERAGE
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 19, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 20, 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
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title
Revision 1.4May 15, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Remark 650 HELIX DETERMINATION METHOD: KABSCH AND SANDER
Remark 700 SHEET DETERMINATION METHOD: KABSCH AND SANDER

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 30S RIBOSOMAL PROTEIN S19


Theoretical massNumber of molelcules
Total (without water)10,4741
Polymers10,4741
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)1 / 21CUMULATIVE RMSD OF STRUCTURES SORTED AFTER TOTAL ENERGY
RepresentativeModel #1

-
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

-
Experimental details

-
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
NMR detailsText: MINIMIZED AVERAGE STRUCTURE.

-
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

-
NMR measurement

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

-
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
Pronto970523)structure solution
X-PLOR3.851)structure solution
MOLMOL2.6)structure solution
PROCHECK / 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: 21 / Conformers submitted total number: 1

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more