[English] 日本語
Yorodumi
- PDB-1c06: SOLUTION STRUCTURE OF RIBOSOMAL PROTEIN S4 DELTA 41, REFINED WITH... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1c06
TitleSOLUTION STRUCTURE OF RIBOSOMAL PROTEIN S4 DELTA 41, REFINED WITH DIPOLAR COUPLINGS (ENSEMBLE OF 16 STRUCTURES)
ComponentsRIBOSOMAL PROTEIN S4 DELTA 41
KeywordsRIBOSOME / TWO SUBDOMAINS / UNIQUE TOPOLOGY / POSSIBLE HELIX-TURN HELIX MOTIF
Function / homology
Function and homology information


ribosomal small subunit biogenesis / small ribosomal subunit / rRNA binding / structural constituent of ribosome / translation / response to antibiotic
Similarity search - Function
Ribosomal protein S4/S9, N-terminal domain / Ribosomal Protein S4 Delta 41; Chain A, domain 1 / RNA-binding S4 domain / Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region; Chain A / Ribosomal protein S4, bacterial-type / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S4, conserved site / Ribosomal protein S4 signature. / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S4/S9, N-terminal ...Ribosomal protein S4/S9, N-terminal domain / Ribosomal Protein S4 Delta 41; Chain A, domain 1 / RNA-binding S4 domain / Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region; Chain A / Ribosomal protein S4, bacterial-type / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S4, conserved site / Ribosomal protein S4 signature. / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S4/S9, N-terminal / Ribosomal protein S4/S9 / S4 RNA-binding domain profile. / S4 RNA-binding domain / S4 domain / RNA-binding S4 domain / RNA-binding S4 domain superfamily / Roll / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Small ribosomal subunit protein uS4
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodSOLUTION NMR / HYBRID DGSA PROTOCOL WITHOUT THE DIPOLAR COUPLING RESTRAINTS, ADDITIONAL SA WITH THE DIPOLAR COUPLING RESTRAINTS ADDED
AuthorsMarkus, M.A. / Gerstner, R.B. / Draper, D.E. / Torchia, D.A.
Citation
Journal: J.Mol.Biol. / Year: 1999
Title: Refining the overall structure and subdomain orientation of ribosomal protein S4 delta41 with dipolar couplings measured by NMR in uniaxial liquid crystalline phases.
Authors: Markus, M.A. / Gerstner, R.B. / Draper, D.E. / Torchia, D.A.
#1: Journal: Embo J. / Year: 1998
Title: The solution structure of ribosomal protein S4 delta 41 reveals two subdomains and a positively charged surface that may interact with RNA
Authors: Markus, M.A. / Gerstner, R.B. / Draper, D.E. / Torchia, D.A.
History
DepositionJul 14, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 29, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_oper_list ...pdbx_struct_assembly / pdbx_struct_oper_list / struct_conf / struct_conf_type
Revision 1.4Apr 10, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RIBOSOMAL PROTEIN S4 DELTA 41


Theoretical massNumber of molelcules
Total (without water)18,6241
Polymers18,6241
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)16 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein RIBOSOMAL PROTEIN S4 DELTA 41


Mass: 18624.359 Da / Num. of mol.: 1 / Fragment: S4 DELTA 41 (S4 RESIDUES 42-200)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Plasmid: PET13A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P81288

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-SEPARATED NOESY
1233D 13C-SEPARATED NOESY
1334D 13C-SEPARATED NOESY
141HNHA
255IPAP 15N HSQC
NMR detailsText: THESE STRUCTURES WERE DETERMINED WITH NOE RESTRAINTS FROM MULTIDIMENSIONAL HETERONUCLEAR EXPERIMENTS, DIHEDRAL ANGLE RESTRAINTS BASED ON MEASUREMENTS OF SCALAR COUPLING CONSTANTS, AND DIPOLAR ...Text: THESE STRUCTURES WERE DETERMINED WITH NOE RESTRAINTS FROM MULTIDIMENSIONAL HETERONUCLEAR EXPERIMENTS, DIHEDRAL ANGLE RESTRAINTS BASED ON MEASUREMENTS OF SCALAR COUPLING CONSTANTS, AND DIPOLAR COUPLING RESTRAINTS MEASURED ON SAMPLES IN PARTIALLY ALIGNED PHASES. THE STRUCTURES ARE ARRANGED IN ORDER FROM LOWEST TO HIGHEST X-PLOR ENERGY.

-
Sample preparation

Details
Solution-IDContentsSolvent system
11.1 MM S4 DELTA 41, U-15N,13C; 20 MM D4-ACETATE PH 5.4, 250 MM KCL, 0.1 MM SODIUM AZIDE94% H2O, 6% D2O
20.8 MM S4 DELTA 41, U-15N; 20 MM D4-ACETATE PH 5.4, 250 MM KCL, 0.1 MM SODIUM AZIDE94% H2O, 6% D2O
30.45 MM S4 DELTA 41, U-15N,13C; 20 MM D4-ACETATE PH 5.4, 250 MM KCL99.9% D2O
40.62 MM S4 DELTA 41, 10% 13C; 20 MM D4-ACETATE PH 5.4, 250 MM KCL99.9% D2O
50.10 MM S4 DELTA 41, U-15N; 7 MM D4-ACETATE PH 5.4, 7 MM KH2PO4 PH 6.5, 80 MM KCL, 5% W/V DMPC:DHPC (3:1)93% H2O/7% D2O
60.21 MM S4 DELTA 41, U-15N, 85% 2H; 15N,13C,1H METHIONINE; EPSILON-13C,1H TYROSINE; BETA,GAMMA,DELTA 2H PROLINE; 10 MM KH2PO4 PH 6.5, 300 MM KCL, 0.2 MM SODIUM AZIDE, 2.5 MG/ML PF194% H2O, 6% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1250 mM KCL 5.4AMBIENT 310 K
280 mM KCL 6AMBIENT 310 K
3300 mM KCL 6.5AMBIENT 310 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX7501
Bruker DMXBrukerDMX5002

-
Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.5BRUKERstructure solution
NMRPipe1.7DELAGLIOstructure solution
PIPP4.2.8GARRETTstructure solution
X-PLOR3.8, 4.0BRUNGERrefinement
RefinementMethod: HYBRID DGSA PROTOCOL WITHOUT THE DIPOLAR COUPLING RESTRAINTS, ADDITIONAL SA WITH THE DIPOLAR COUPLING RESTRAINTS ADDED
Software ordinal: 1
Details: SUMMARY OF RESTRAINTS: 2170 NOE, 86 HYDROGEN BOND, 114 DIHEDRAL ANGLE, AND 101 DIPOLAR COUPLINGS
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 16

+
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