[English] 日本語
Yorodumi
- PDB-8aa8: 30S ribosomal protein S24e from Thermococcus barophilus -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8aa8
Title30S ribosomal protein S24e from Thermococcus barophilus
Components30S ribosomal protein S24e
KeywordsGENE REGULATION / high pressure adaptation protein dynamics structural constituent of ribosome
Function / homology
Function and homology information


ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex
Similarity search - Function
RRM (RNA recognition motif) domain / Ribosomal S24e conserved site / Ribosomal protein S24e signature. / Ribosomal protein S24e / Ribosomal protein S24e / Ribosomal protein L23/L15e core domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Small ribosomal subunit protein eS24
Similarity search - Component
Biological speciesThermococcus barophilus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 Å
AuthorsCalio, A. / Hoh, F.
Funding support France, 2items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)17-CE11-0012-01 France
Centre National de la Recherche Scientifique (CNRS)MITI OriginsUnderPressure et LifeAdapt France
CitationJournal: To Be Published
Title: 30S ribosomal protein S24e from Thermococcus barophilus at 1.7A
Authors: Calio, A. / Hoh, F.
History
DepositionJun 30, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 12, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 30S ribosomal protein S24e
B: 30S ribosomal protein S24e


Theoretical massNumber of molelcules
Total (without water)23,3332
Polymers23,3332
Non-polymers00
Water1,71195
1
A: 30S ribosomal protein S24e


Theoretical massNumber of molelcules
Total (without water)11,6661
Polymers11,6661
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 30S ribosomal protein S24e


Theoretical massNumber of molelcules
Total (without water)11,6661
Polymers11,6661
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)24.306, 35.067, 48.897
Angle α, β, γ (deg.)91.36, 89.95, 92.18
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein 30S ribosomal protein S24e


Mass: 11666.480 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus barophilus (archaea) / Gene: rps24e, TBCH5v1_2408 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0S1XER1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / 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: 2.18 Å3/Da / Density % sol: 43.49 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 0,1 M MES pH 6,5, 30 %(v/v) PEG 300

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.96 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 23, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96 Å / Relative weight: 1
ReflectionResolution: 1.71→48.88 Å / Num. obs: 15519 / % possible obs: 92 % / Redundancy: 1.72 % / CC1/2: 0.936 / Net I/σ(I): 1.6
Reflection shellResolution: 1.71→1.83 Å / Num. unique obs: 2560 / CC1/2: 0.255

-
Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7ZVM

7zvm


Resolution: 1.71→48.88 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.949 / SU B: 4.007 / SU ML: 0.062 / Cross valid method: THROUGHOUT / ESU R: 0.052 / ESU R Free: 0.026 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22514 785 5 %RANDOM
Rwork0.18578 ---
obs0.18775 14883 89.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.822 Å2
Baniso -1Baniso -2Baniso -3
1--13.21 Å25.07 Å2-0.7 Å2
2--2.01 Å21.75 Å2
3---11.19 Å2
Refinement stepCycle: 1 / Resolution: 1.71→48.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1300 0 0 95 1395
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0121296
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161221
X-RAY DIFFRACTIONr_angle_refined_deg1.4851.6541746
X-RAY DIFFRACTIONr_angle_other_deg0.5281.5552837
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7235160
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.5611010
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.02210234
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0640.2197
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021453
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02251
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.22.591649
X-RAY DIFFRACTIONr_mcbond_other4.1972.59649
X-RAY DIFFRACTIONr_mcangle_it4.4533.9806
X-RAY DIFFRACTIONr_mcangle_other4.4513.9807
X-RAY DIFFRACTIONr_scbond_it5.1622.829647
X-RAY DIFFRACTIONr_scbond_other5.1622.828647
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.4394.165941
X-RAY DIFFRACTIONr_long_range_B_refined5.06653.6255138
X-RAY DIFFRACTIONr_long_range_B_other5.07653.4395084
X-RAY DIFFRACTIONr_rigid_bond_restr5.91232517
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.71→1.753 Å
RfactorNum. reflection% reflection
Rfree0.353 11 -
Rwork0.288 141 -
obs--11.54 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.12040.33740.17252.3838-0.15520.9432-0.0130.0130.0063-0.09790.00870.0389-0.0147-0.06740.00430.0146-0.00560.01510.0102-0.01190.028814.642127.53233.6893
21.23880.18570.311.79260.50281.7205-0.0106-0.03670.0295-0.00790.0179-0.0431-0.0256-0.0038-0.00730.01380.0040.01830.03320.00370.02714.962614.05369.2483
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 93
2X-RAY DIFFRACTION2B1 - 72

+
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