[English] 日本語
Yorodumi
- PDB-6i6i: Circular permutant of ribosomal protein S6, adding 6aa to C termi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6i6i
TitleCircular permutant of ribosomal protein S6, adding 6aa to C terminal of P68-69, L75A mutant
Components30S ribosomal protein S6,30S ribosomal protein S6
KeywordsRIBOSOMAL PROTEIN / Circular permutant / strand swap / local unfolding / cis-proline.
Function / homology
Function and homology information


small ribosomal subunit rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / cytoplasm
Similarity search - Function
Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein S6 / Ribosomal protein S6 / Ribosomal protein S6 superfamily / Translation elongation factor EF1B/ribosomal protein S6
Similarity search - Domain/homology
Small ribosomal subunit protein bS6 / Small ribosomal subunit protein bS6
Similarity search - Component
Biological speciesThermus thermophilus HB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsWang, H. / Logan, D.T. / Oliveberg, M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Exposing the distinctive modular behavior of beta-strands and alpha-helices in folded proteins.
Authors: Wang, H. / Logan, D.T. / Danielsson, J. / Oliveberg, M.
History
DepositionNov 15, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 27, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 9, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Dec 23, 2020Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Revision 1.3Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 30S ribosomal protein S6,30S ribosomal protein S6
B: 30S ribosomal protein S6,30S ribosomal protein S6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0854
Polymers23,8932
Non-polymers1922
Water1,20767
1
A: 30S ribosomal protein S6,30S ribosomal protein S6

A: 30S ribosomal protein S6,30S ribosomal protein S6


Theoretical massNumber of molelcules
Total (without water)23,8932
Polymers23,8932
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_454-x-1,y,-z-1/21
Buried area2450 Å2
ΔGint-36 kcal/mol
Surface area10760 Å2
MethodPISA
2
B: 30S ribosomal protein S6,30S ribosomal protein S6
hetero molecules

B: 30S ribosomal protein S6,30S ribosomal protein S6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2776
Polymers23,8932
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area2420 Å2
ΔGint-36 kcal/mol
Surface area10820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.651, 48.659, 132.740
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein 30S ribosomal protein S6,30S ribosomal protein S6 / TS9


Mass: 11946.521 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus HB8 (bacteria) / Gene: rpsF, TTHA0245, rpsF, rps6, TT_C1740 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q5SLP8, UniProt: P62666
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 1.75 Å3/Da / Density % sol: 29.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Lithium sulphate 0.1 M Tris pH 8.5 40% v/v PEG 400

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 9, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.5→44.25 Å / Num. obs: 25756 / % possible obs: 99.6 % / Redundancy: 11.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.026 / Rrim(I) all: 0.09 / Net I/σ(I): 12.5 / Num. measured all: 304038 / Scaling rejects: 316
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.5-1.5211.20.6312370.6550.1930.65999.2
8.2-44.259.50.0631770.9950.0210.06693.5

-
Processing

Software
NameVersionClassification
Aimless0.5.32data scaling
REFMAC5.8.0158refinement
PDB_EXTRACT3.24data extraction
iMOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Ris

1ris


Resolution: 1.5→44.25 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.947 / SU B: 1.988 / SU ML: 0.071 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.088 / ESU R Free: 0.092
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.233 1274 5 %RANDOM
Rwork0.19 ---
obs0.192 24441 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 71.48 Å2 / Biso mean: 27.15 Å2 / Biso min: 17.29 Å2
Baniso -1Baniso -2Baniso -3
1--0.4 Å20 Å20 Å2
2--0.8 Å20 Å2
3----0.4 Å2
Refinement stepCycle: final / Resolution: 1.5→44.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1574 0 10 67 1651
Biso mean--37.97 33.82 -
Num. residues----192
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0191606
X-RAY DIFFRACTIONr_bond_other_d0.0030.021532
X-RAY DIFFRACTIONr_angle_refined_deg1.8921.982172
X-RAY DIFFRACTIONr_angle_other_deg1.01533528
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4915190
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.73923.40988
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.69315292
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2991522
X-RAY DIFFRACTIONr_chiral_restr0.1170.2240
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0211764
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02330
LS refinement shellResolution: 1.497→1.536 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 89 -
Rwork0.367 1760 -
all-1849 -
obs--99.3 %

+
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