[English] 日本語
Yorodumi
- PDB-3rf2: Crystal Structure of 30S Ribosomal Protein S8 from Aquifex Aeolicus -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3rf2
TitleCrystal Structure of 30S Ribosomal Protein S8 from Aquifex Aeolicus
Components30S ribosomal protein S8
KeywordsRIBOSOMAL PROTEIN / RNA-binding protein / Aquifex aeolicus / hyperthermophilic bacterium / Ribosome
Function / homology
Function and homology information


cytosolic small ribosomal subunit / rRNA binding / structural constituent of ribosome / translation
Similarity search - Function
Dna Ligase; domain 1 - #10 / Dna Ligase; domain 1 / Ribosomal protein S8 / Ribosomal protein S8 superfamily / Ribosomal protein S8 / Ribosomal protein S8 signature. / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
30S ribosomal protein S8
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD, MOLECULAR REPLACEMENT / MAD / molecular replacement / Resolution: 2.16 Å
AuthorsMenichelli, E. / Williamson, J.R.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: The Structure of Aquifex aeolicus Ribosomal Protein S8 Reveals a Unique Subdomain that Contributes to an Extremely Tight Association with 16S rRNA.
Authors: Menichelli, E. / Edgcomb, S.P. / Recht, M.I. / Williamson, J.R.
History
DepositionApr 5, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 16, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2011Group: Database references
Revision 1.2Feb 1, 2012Group: Database references
Revision 1.3Oct 25, 2017Group: Advisory / Author supporting evidence
Category: pdbx_struct_assembly_auth_evidence / pdbx_unobs_or_zero_occ_residues
Revision 1.4Feb 21, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_residues / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 30S ribosomal protein S8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9756
Polymers19,4951
Non-polymers4805
Water91951
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.235, 96.235, 37.614
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-197-

HOH

DetailsAUTHORS STATE THAT THE PROTEIN WAS CHARACTERIZED BY SIZE EXCLUSION CHROMATOGRAPHY AND IN SOLUTION IT IS FOUND TO BE A MONOMER.

-
Components

#1: Protein 30S ribosomal protein S8 /


Mass: 19494.951 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Gene: rpsH, aq_1651 / Plasmid: pET11c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus (DE3)-RIL / References: UniProt: O67566
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 51 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 44.93 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 4.6
Details: 40% PEG 400, 0.1M sodium acetate, 0.2M lithium sulphate, pH 4.6, VAPOR DIFFUSION, temperature 295K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRL BL11-110.979
SYNCHROTRONSSRL BL11-120.978, 0.918, 0.979
Detector
TypeIDDetectorDate
MARMOSAIC 325 mm CCD1CCDJun 23, 2010
MARMOSAIC 325 mm CCD2CCDApr 29, 2010
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Side scattering bent cube-root I-beam single crystal; asymmetric cut 4.965 degsSINGLE WAVELENGTHMx-ray1
2Side scattering bent cube-root I-beam single crystal; asymmetric cut 4.965 degsMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
20.9781
30.9181
ReflectionRedundancy: 18.7 % / Av σ(I) over netI: 38.51 / Number: 208216 / Rmerge(I) obs: 0.122 / Χ2: 1.07 / D res high: 2.6 Å / D res low: 50 Å / Num. obs: 11135 / % possible obs: 98.6
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.65099.710.0891.41718.9
4.455.610010.0911.15919.8
3.884.4510010.1021.04419.9
3.533.8810010.1211.00120
3.283.5310010.1461.01820
3.083.2810010.1781.01919.8
2.933.0899.510.2321.00919.4
2.82.9399.510.2611.05317.7
2.692.896.410.3480.98816.2
2.62.6990.310.3650.96614.6
ReflectionResolution: 2.16→50 Å / Num. obs: 9918 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 12.3 % / Rmerge(I) obs: 0.062 / Χ2: 0.994 / Net I/σ(I): 14.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.16-2.244.60.2369400.941,296.1
2.24-2.334.90.2219450.9561,298.3
2.33-2.4310.30.1729670.9241,299.3
2.43-2.5614.50.169720.9361,2100
2.56-2.7214.80.1279930.9411,2100
2.72-2.93150.0999831.0771,2100
2.93-3.2314.90.0779920.9611,2100
3.23-3.6914.80.06310061.0361,2100
3.69-4.6514.60.05710201.0541,2100
4.65-5013.40.04311001.0151,299.4

-
Phasing

Phasing
Method
MAD
molecular replacement
Phasing MADD res high: 3 Å / D res low: 1000 Å / FOM : 0.62 / Reflection: 3907
Phasing MAD set site
IDCartn x (Å)Cartn y (Å)Cartn z (Å)Atom type symbolB isoOccupancy
163.19541.3434.176SE601.38
268.01747.2230.809SE440.99
348.4220.6921.535SE601.23
460.41981.8914.652SE600.83
548.81168.0692.869SE600.97
684.735.1351.363SE601.14
70.44517.7932.427SE54.40.52
Phasing MAD shell
Resolution (Å)FOM Reflection
10.95-10000.81207
6.86-10.950.81336
5.35-6.860.78414
4.53-5.350.71486
4-4.530.66541
3.62-40.59592
3.33-3.620.52654
3.1-3.330.4677
Phasing MR
Highest resolutionLowest resolution
Rotation2.2 Å35.03 Å
Translation2.2 Å35.03 Å
Phasing dmFOM : 0.72 / FOM acentric: 0.73 / FOM centric: 0.69 / Reflection: 3900 / Reflection acentric: 2980 / Reflection centric: 920
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
3-3.20.470.50.35701582119
3.2-3.80.650.670.581151931220
3.8-4.30.770.80.69649508141
4.3-5.40.850.860.79659497162
5.4-8.60.870.890.82543367176

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.2.4phasing
SOLVEphasing
RESOLVE2.15phasing
PHENIX1.7_650refinement
PDB_EXTRACT3.1data extraction
Blu-Icedata collection
RefinementMethod to determine structure: MAD, MOLECULAR REPLACEMENT / Resolution: 2.16→30.432 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.7713 / SU ML: 0.31 / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2674 971 9.98 %RANDOM
Rwork0.2231 ---
all0.2275 9730 --
obs0.2275 9730 97.83 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.458 Å2 / ksol: 0.361 e/Å3
Displacement parametersBiso max: 170.6 Å2 / Biso mean: 51.4623 Å2 / Biso min: 16.08 Å2
Baniso -1Baniso -2Baniso -3
1--6.4335 Å2-0 Å20 Å2
2---6.4335 Å2-0 Å2
3---12.867 Å2
Refinement stepCycle: LAST / Resolution: 2.16→30.432 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1333 0 25 51 1409
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071376
X-RAY DIFFRACTIONf_angle_d0.9871842
X-RAY DIFFRACTIONf_chiral_restr0.065193
X-RAY DIFFRACTIONf_plane_restr0.005226
X-RAY DIFFRACTIONf_dihedral_angle_d14.451536
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.16-2.27410.34321300.29021138126892
2.2741-2.41650.32671310.26271193132495
2.4165-2.6030.30371370.26951234137198
2.603-2.86470.34091380.25391258139699
2.8647-3.27890.2651400.23512571397100
3.2789-4.12940.24851450.195113031448100
4.1294-30.43520.23131500.203313761526100
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)
10.27320.01780.11170.067-0.01590.06670.1529-0.4852-0.75490.27750.18540.36560.1649-0.3597-0.03760.2320.01260.00840.44560.27470.64661.0652-26.136914.4411
20.03540.0335-0.09660.0449-0.1040.27810.20180.3171-0.5303-0.1175-0.12890.0269-0.09070.22620.05650.18730.1195-0.04940.219-0.0590.5785.9316-26.27043.1725
30.01730.00740.00990.00510.00390.02070.0157-0.0467-0.0793-0.03880.0180.00030.08020.00880.01980.17740.1261-0.4170.25840.49811.595714.2965-40.720816.2319
40.01510.0336-0.0560.0601-0.08840.12320.0954-0.0936-0.3717-0.00220.07350.20050.1402-0.2530.01710.2994-0.2127-0.20090.13360.49341.20975.8284-36.365916.5536
50.2524-0.10660.03950.52750.23360.2562-0.0274-0.3397-0.07350.24550.05950.2804-0.219-0.06990.05280.35780.0429-0.02590.28150.05520.10393.2977-16.432413.0896
60.91580.0060.24660.81340.51690.58470.17670.5952-0.3902-0.36860.03080.09330.16230.10750.01530.26070.0442-0.03690.33-0.06890.1717-5.5706-15.3831-3.4677
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 4:30)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 31:53)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 54:69)
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 70:98)
5X-RAY DIFFRACTION5CHAIN A AND (RESSEQ 99:120)
6X-RAY DIFFRACTION6CHAIN A AND (RESSEQ 121:168)

+
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