[English] 日本語
Yorodumi
- PDB-5xe2: Endoribonuclease from Mycobacterial species -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5xe2
TitleEndoribonuclease from Mycobacterial species
ComponentsEndoribonuclease MazF4
KeywordsHYDROLASE / endonuclease
Function / homology
Function and homology information


rRNA catabolic process / mRNA catabolic process / enzyme inhibitor activity / RNA endonuclease activity / Hydrolases; Acting on ester bonds / DNA binding
Similarity search - Function
mRNA interferase PemK-like / PemK-like, MazF-like toxin of type II toxin-antitoxin system / Plasmid maintenance toxin/Cell growth inhibitor
Similarity search - Domain/homology
Endoribonuclease MazF4
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsAhn, D.-H. / Lee, K.-Y. / Lee, S.J. / Yoon, H.J. / Kim, S.-J. / Lee, B.-J.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
National Research foundation of Korea (NRF)2015R1A2A1A05001894 Korea, Republic Of
National Research Foundation of Korea (NRF)2014K1A3A1A19067618 Korea, Republic Of
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Structural analyses of the MazEF4 toxin-antitoxin pair in Mycobacterium tuberculosis provide evidence for a unique extracellular death factor.
Authors: Ahn, D.H. / Lee, K.Y. / Lee, S.J. / Park, S.J. / Yoon, H.J. / Kim, S.J. / Lee, B.J.
History
DepositionMar 31, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 11, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Feb 7, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 22, 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: Endoribonuclease MazF4


Theoretical massNumber of molelcules
Total (without water)11,6971
Polymers11,6971
Non-polymers00
Water1,06359
1
A: Endoribonuclease MazF4

A: Endoribonuclease MazF4


Theoretical massNumber of molelcules
Total (without water)23,3952
Polymers23,3952
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area1840 Å2
ΔGint-10 kcal/mol
Surface area10220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.475, 65.548, 57.390
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein Endoribonuclease MazF4 / Toxin MazF4 / mRNA interferase MazF-mt7


Mass: 11697.274 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: mazF4, mazF-mt7, Rv1495, MTCY277.17 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P9WII5, Hydrolases; Acting on ester bonds
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 1.99 Å3/Da / Density % sol: 38.16 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 7
Details: 0.2M sodium malonate at pH 7.0 and 20% (w/v) polyethylene glycol 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.01→30 Å / Num. obs: 7261 / % possible obs: 97.5 % / Redundancy: 7.9 % / Rmerge(I) obs: 0.146 / Rpim(I) all: 0.054 / Rrim(I) all: 0.157 / Χ2: 1.923 / Net I/σ(I): 5.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.87-1.97.70.7340.8840.2730.7870.79992.5
1.9-1.9480.6640.890.2410.7090.98693.9
1.94-1.9780.5440.9370.1970.5811.02595.5
1.97-2.0180.5520.8970.2040.591.11197.6
2.01-2.067.90.440.9340.1650.4711.29797.5
2.06-2.117.80.4170.9480.1540.4461.56498.3
2.11-2.167.40.3840.9350.1450.4131.76497.8
2.16-2.227.40.3560.9630.1350.3821.81996.8
2.22-2.288.30.3390.9720.1210.3611.87798
2.28-2.368.60.2910.9790.1050.311.85596.9
2.36-2.448.30.2730.9740.0980.2912.05698.1
2.44-2.548.20.2480.9850.0910.2651.94998.6
2.54-2.6580.2070.9890.0770.2212.05997.8
2.65-2.797.10.1980.9830.0770.2132.60398.6
2.79-2.977.60.1750.9850.0670.1882.85797.6
2.97-3.28.20.1430.9870.0510.1522.47498.9
3.2-3.5280.1190.9940.0440.1282.82599
3.52-4.037.20.1030.9910.040.1112.82399.2
4.03-5.077.90.0860.9940.0310.0922.58699.2
5.07-307.70.0770.9940.0290.0821.9797.6

-
Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-2000data scaling
PDB_EXTRACT3.22data extraction
MOLREPphasing
HKLdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XE3

5xe3


Resolution: 2.01→30 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.925 / SU B: 4.373 / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.237 / ESU R Free: 0.171
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES
RfactorNum. reflection% reflectionSelection details
Rfree0.2227 307 4.8 %RANDOM
Rwork0.2037 ---
obs0.2046 6119 99.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 57.44 Å2 / Biso mean: 23.868 Å2 / Biso min: 12.97 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2---0.13 Å2-0 Å2
3---0.11 Å2
Refinement stepCycle: final / Resolution: 2.01→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms801 0 0 59 860
Biso mean---33.14 -
Num. residues----104
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.02818
X-RAY DIFFRACTIONr_bond_other_d0.0030.02787
X-RAY DIFFRACTIONr_angle_refined_deg1.1821.9621120
X-RAY DIFFRACTIONr_angle_other_deg0.87431802
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7575102
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.31323.52934
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.88215127
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.051157
X-RAY DIFFRACTIONr_chiral_restr0.060.2132
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021918
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02179
LS refinement shellResolution: 2.01→2.062 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.375 21 -
Rwork0.217 412 -
all-433 -
obs--89.83 %

+
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