[English] 日本語
Yorodumi
- PDB-4oun: Crystal Structure of Mini-ribonuclease 3 from Bacillus subtilis -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4oun
TitleCrystal Structure of Mini-ribonuclease 3 from Bacillus subtilis
ComponentsMini-ribonuclease 3
KeywordsHYDROLASE / RNase III domain-like / Ribonuclease / RNA binding
Function / homology
Function and homology information


ribonuclease III activity / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / RNA nuclease activity / rRNA processing / rRNA binding / cytoplasm
Similarity search - Function
Mini-ribonuclease 3 family / Ribonuclease III domain / Ribonuclease iii, N-terminal Endonuclease Domain; Chain A / Ribonuclease III domain / Ribonuclease III family / Ribonuclease III domain / Ribonuclease III, endonuclease domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesBacillus subtilis subsp. subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsChojnowski, G. / Czarnecka, J. / Nowak, E. / Pianka, D. / Glow, D. / Sabala, I. / Skowronek, K. / Nowotny, M. / Bujnicki, J.M.
CitationJournal: Nucleic Acids Res. / Year: 2015
Title: Sequence-specific cleavage of dsRNA by Mini-III RNase
Authors: Glow, D. / Pianka, D. / Sulej, A.A. / Kozlowski, L.P. / Czarnecka, J. / Chojnowski, G. / Skowronek, K.J. / Bujnicki, J.M.
History
DepositionFeb 18, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 4, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 22, 2015Group: Database references
Revision 1.2Dec 18, 2019Group: Data collection / Database references / Category: reflns_shell / struct_ref_seq_dif
Item: _reflns_shell.Rmerge_I_obs / _struct_ref_seq_dif.details
Revision 1.3Nov 8, 2023Group: 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: Mini-ribonuclease 3


Theoretical massNumber of molelcules
Total (without water)18,4231
Polymers18,4231
Non-polymers00
Water64936
1
A: Mini-ribonuclease 3

A: Mini-ribonuclease 3


Theoretical massNumber of molelcules
Total (without water)36,8452
Polymers36,8452
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area2600 Å2
ΔGint-24 kcal/mol
Surface area12790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.092, 62.028, 89.388
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-216-

HOH

21A-222-

HOH

-
Components

#1: Protein Mini-ribonuclease 3 / Mini-3 / Mini-RNase 3 / Mini-RNase III / Mini-III


Mass: 18422.740 Da / Num. of mol.: 1 / Mutation: E126Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis (bacteria)
Strain: 168 / Gene: mrnC, yazC, BSU00950 / Production host: Escherichia coli (E. coli)
References: UniProt: O31418, Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 1.55 Å3/Da / Density % sol: 20.43 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2M sodium acetate trihydrate, 0.1M TRIS, 30% PEG4000, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.917152 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 24, 2013
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.917152 Å / Relative weight: 1
ReflectionResolution: 1.8→44.7 Å / Num. all: 10956 / Num. obs: 10939 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Biso Wilson estimate: 36.163 Å2 / Rmerge(I) obs: 0.091 / Χ2: 0.964 / Net I/σ(I): 17.17
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.8-1.910.9221.42.0422773174417321.46899.3
1.91-2.040.9593.2820472163816350.88499.8
2.04-2.20.9896.0120736153215310.4799.9
2.2-2.410.99510.0818657139613940.25699.9
2.41-2.70.99914.8416296129512950.153100
2.7-3.110.99924.9115653115011500.093100
3.11-3.810.99938.98121709649640.056100
3.81-5.360.99955.94100867787770.03999.9
5.36-44.69158.1152724614610.04100

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.8 Å44.69 Å
Translation1.8 Å44.69 Å

-
Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.5.0phasing
REFMAC5.8.0049refinement
PDB_EXTRACT3.14data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1U61

1u61


Resolution: 1.8→44.69 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.938 / SU B: 6.413 / SU ML: 0.176 / Cross valid method: THROUGHOUT / σ(I): 2 / ESU R: 0.155 / ESU R Free: 0.156 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2676 547 5 %RANDOM
Rwork0.206 ---
obs0.2092 10939 99.84 %-
all-10956 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 95.64 Å2 / Biso mean: 41.917 Å2 / Biso min: 21.79 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å2-0 Å2
2---0.05 Å20 Å2
3----0 Å2
Refinement stepCycle: LAST / Resolution: 1.8→44.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1009 0 0 36 1045
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0191027
X-RAY DIFFRACTIONr_angle_refined_deg1.5421.9571378
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0425123
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.58224.11851
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.35815190
X-RAY DIFFRACTIONr_dihedral_angle_4_deg29.895156
X-RAY DIFFRACTIONr_chiral_restr0.1140.2153
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02766
X-RAY DIFFRACTIONr_mcbond_it3.3873.841498
X-RAY DIFFRACTIONr_mcangle_it4.8165.719619
X-RAY DIFFRACTIONr_scbond_it5.0464.469529
LS refinement shellResolution: 1.799→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.481 39 -
Rwork0.43 754 -
all-793 -
obs--98.75 %

+
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