[English] 日本語
Yorodumi
- PDB-7did: Mycoplasma genitalium RNase R in complex with ribose methylated s... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7did
TitleMycoplasma genitalium RNase R in complex with ribose methylated single-stranded RNA
Components
  • RNA (5'-R(*AP*AP*AP*A)-3')
  • Ribonuclease R
KeywordsHYDROLASE/RNA / RNA hydrolase / 2'-O-methylation sensitive / HYDROLASE / HYDROLASE-RNA complex
Function / homology
Function and homology information


exoribonuclease II activity / exoribonuclease II / mRNA catabolic process / RNA binding / cytosol
Similarity search - Function
Ribonuclease R / Ribonuclease II/ribonuclease R / Ribonuclease II/R, conserved site / Ribonuclease II family signature. / : / Ribonuclease II/R / RNB domain / RNB / Cold shock domain / Cold shock protein domain ...Ribonuclease R / Ribonuclease II/ribonuclease R / Ribonuclease II/R, conserved site / Ribonuclease II family signature. / : / Ribonuclease II/R / RNB domain / RNB / Cold shock domain / Cold shock protein domain / S1 domain profile. / Ribosomal protein S1-like RNA-binding domain / S1 RNA binding domain / S1 domain / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
RNA / Ribonuclease R
Similarity search - Component
Biological speciesMycoplasma genitalium G37 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsAbula, A. / Quan, X. / Li, X. / Yang, T. / Li, T. / Chen, Q. / Ji, X.
CitationJournal: Nucleic Acids Res. / Year: 2021
Title: Molecular mechanism of RNase R substrate sensitivity for RNA ribose methylation.
Authors: Abula, A. / Li, X. / Quan, X. / Yang, T. / Liu, Y. / Guo, H. / Li, T. / Ji, X.
History
DepositionNov 18, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 17, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 14, 2021Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 19, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 29, 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: Ribonuclease R
C: RNA (5'-R(*AP*AP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,9063
Polymers86,8812
Non-polymers241
Water8,881493
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2260 Å2
ΔGint-13 kcal/mol
Surface area30780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.286, 80.784, 175.735
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Ribonuclease R / RNase R / VacB protein homolog


Mass: 85595.555 Da / Num. of mol.: 1 / Mutation: D284A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycoplasma genitalium G37 (bacteria) / Strain: G-37 / Gene: rnr, vacB, MG104 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: P47350, exoribonuclease II
#2: RNA chain RNA (5'-R(*AP*AP*AP*A)-3')


Mass: 1285.893 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mycoplasma genitalium G37 (bacteria)
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 493 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.83 Å3/Da / Density % sol: 56.52 %
Crystal growTemperature: 295 K / Method: microbatch / Details: 100 mM KCl, 100 mM HEPES (pH 6.8), 15% PEG 5000MME

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 78483 / % possible obs: 99.9 % / Redundancy: 13.2 % / Rmerge(I) obs: 0.148 / Net I/σ(I): 18
Reflection shellResolution: 1.9→1.93 Å / Mean I/σ(I) obs: 1 / Num. unique obs: 3891 / Rrim(I) all: 2.936

-
Processing

Software
NameVersionClassification
PHENIX1.10_2148refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XGU

5xgu


Resolution: 1.9→29.979 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 24.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2218 1995 2.55 %
Rwork0.1881 76281 -
obs0.189 78276 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 116.49 Å2 / Biso mean: 46.0262 Å2 / Biso min: 21.1 Å2
Refinement stepCycle: final / Resolution: 1.9→29.979 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5196 86 1 493 5776
Biso mean--39.6 49.03 -
Num. residues----648
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0125405
X-RAY DIFFRACTIONf_angle_d1.0097347
X-RAY DIFFRACTIONf_chiral_restr0.067851
X-RAY DIFFRACTIONf_plane_restr0.006929
X-RAY DIFFRACTIONf_dihedral_angle_d15.5483261
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9-1.94720.40591390.3518528398
1.9472-1.99980.34211420.30545422100
1.9998-2.05870.31851410.28085389100
2.0587-2.12510.31671420.2555434100
2.1251-2.2010.26191410.22915373100
2.201-2.28910.26871410.21195409100
2.2891-2.39330.25581420.20015434100
2.3933-2.51940.23091430.19325421100
2.5194-2.67710.21991410.1885440100
2.6771-2.88370.24391430.19455464100
2.8837-3.17360.22771430.19415452100
3.1736-3.63210.21221420.1765501100
3.6321-4.57350.1721460.15325549100
4.5735-29.970.19411490.1665571099
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)
11.85470.90370.55491.216-0.52080.9071-0.0175-0.01810.41130.1117-0.00310.2356-0.1909-0.14710.00020.26360.0099-0.01710.2715-0.01950.3204-24.6253-7.57054.3733
21.08690.1932-0.97040.75460.53221.38680.06520.10540.062-0.0084-0.0224-0.0932-0.06290.12170.00610.2195-0.0273-0.00310.2810.00080.2666-7.5075-14.22128.3352
31.8730.32450.42162.050.32882.0706-0.0727-0.2231-0.01420.36930.0124-0.11850.16710.0886-0.00110.37810.0149-0.04690.2628-0.03560.2826-6.7136-5.573947.7015
41.04040.82020.5091.14050.51171.2809-0.0876-0.10960.28960.04440.01120.2381-0.0623-0.2615-0.00030.23750.0132-0.01510.28140.0090.2761-26.913-11.859831.4631
50.0074-0.01940.00240.0269-0.00920.01460.0705-0.0451-0.51630.29650.2138-0.56771.00120.6208-0.00030.8362-0.0739-0.24650.76020.14921.4781-19.407-9.663638.8457
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 82 through 170 )A82 - 170
2X-RAY DIFFRACTION2chain 'A' and (resid 171 through 250 )A171 - 250
3X-RAY DIFFRACTION3chain 'A' and (resid 251 through 427 )A251 - 427
4X-RAY DIFFRACTION4chain 'A' and (resid 428 through 725 )A428 - 725
5X-RAY DIFFRACTION5chain 'C' and (resid 5 through 8 )C5 - 8

+
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