[English] 日本語
Yorodumi
- PDB-5xgu: Escherichia coli. RNase R -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5xgu
TitleEscherichia coli. RNase R
ComponentsRibonuclease R
KeywordsHYDROLASE / exoribonuclease
Function / homology
Function and homology information


exoribonuclease II / exoribonuclease II activity / RNA binding / cytoplasm
Similarity search - Function
Ribonuclease R winged-helix domain / Ribonuclease R winged-helix domain / RNase II/RNase R, cold shock domain / Ribonuclease B, N-terminal OB domain / Ribonuclease B OB domain / Cold shock domain / Ribonuclease R / Ribonuclease II/ribonuclease R / Ribonuclease II/R, conserved site / Ribonuclease II family signature. ...Ribonuclease R winged-helix domain / Ribonuclease R winged-helix domain / RNase II/RNase R, cold shock domain / Ribonuclease B, N-terminal OB domain / Ribonuclease B OB domain / Cold shock domain / Ribonuclease R / Ribonuclease II/ribonuclease R / Ribonuclease II/R, conserved site / Ribonuclease II family signature. / Ribonuclease II/R / RNB domain / RNB / RNA-binding domain, S1 / 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
Biological speciesEscherichia coli DEC6A (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.846 Å
AuthorsChu, L.Y. / Hsieh, T.J. / Yuan, H.S.
CitationJournal: Nucleic Acids Res. / Year: 2017
Title: Structural insights into RNA unwinding and degradation by RNase R.
Authors: Chu, L.Y. / Hsieh, T.J. / Golzarroshan, B. / Chen, Y.P. / Agrawal, S. / Yuan, H.S.
History
DepositionApr 17, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 18, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2017Group: 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 1.2Nov 29, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Ribonuclease R
A: Ribonuclease R
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,7214
Polymers146,6732
Non-polymers492
Water30,2831681
1
A: Ribonuclease R
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,3612
Polymers73,3361
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-8 kcal/mol
Surface area29750 Å2
MethodPISA
2
B: Ribonuclease R
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,3612
Polymers73,3361
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-8 kcal/mol
Surface area30350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.691, 120.863, 83.626
Angle α, β, γ (deg.)90.00, 91.61, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Ribonuclease R / RNase R


Mass: 73336.336 Da / Num. of mol.: 2 / Fragment: UNP residues 87-725 / Mutation: A45V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli DEC6A (bacteria) / Gene: rnr, ECDEC6A_5034 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: H4USN4, exoribonuclease II
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1681 / 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: 2.55 Å3/Da / Density % sol: 51.83 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 8% v/v Tacimate, pH 6.0, 10 % w/v Polyethylene glycol 3,350

-
Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Oct 24, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→30 Å / Num. obs: 124382 / % possible obs: 99.14 % / Redundancy: 4.5 % / Rsym value: 0.089 / Net I/σ(I): 11.8
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 3.7 / Num. unique obs: 48331 / Rsym value: 0.445 / % possible all: 99.14

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2VNU

2vnu


Resolution: 1.846→29.671 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2362 2005 1.61 %
Rwork0.1872 --
obs0.188 124300 99.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.846→29.671 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9959 0 2 1681 11642
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00610152
X-RAY DIFFRACTIONf_angle_d0.67213710
X-RAY DIFFRACTIONf_dihedral_angle_d13.7416148
X-RAY DIFFRACTIONf_chiral_restr0.0451500
X-RAY DIFFRACTIONf_plane_restr0.0041799
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8457-1.89180.26861220.22217857X-RAY DIFFRACTION89
1.8918-1.9430.24511490.22288756X-RAY DIFFRACTION100
1.943-2.00020.25351480.21878757X-RAY DIFFRACTION100
2.0002-2.06470.28211420.21338757X-RAY DIFFRACTION100
2.0647-2.13850.26271450.2038777X-RAY DIFFRACTION100
2.1385-2.22410.22621400.19568797X-RAY DIFFRACTION100
2.2241-2.32520.22881410.18878832X-RAY DIFFRACTION100
2.3252-2.44780.25471440.19068803X-RAY DIFFRACTION100
2.4478-2.60110.22361500.19968757X-RAY DIFFRACTION100
2.6011-2.80180.24761470.19938814X-RAY DIFFRACTION100
2.8018-3.08340.28321420.20058847X-RAY DIFFRACTION100
3.0834-3.5290.23731440.18258810X-RAY DIFFRACTION100
3.529-4.44380.21341460.15338836X-RAY DIFFRACTION100
4.4438-29.67480.20321450.17298895X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -12.4535 Å / Origin y: 44.8802 Å / Origin z: -60.9634 Å
111213212223313233
T0.1264 Å20.0028 Å2-0.0031 Å2-0.1212 Å2-0.0288 Å2--0.1487 Å2
L0.059 °2-0.0051 °2-0.0131 °2-0.1242 °2-0.1782 °2--0.3761 °2
S-0.0007 Å °0.014 Å °-0.0072 Å °-0.0233 Å °0.0326 Å °0.0522 Å °-0.0084 Å °-0.0744 Å °-0.0337 Å °
Refinement TLS groupSelection details: all

+
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