[English] 日本語
Yorodumi
- PDB-5hjz: Structure of M. tuberculosis MazF-mt1 (Rv2801c) in complex with RNA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5hjz
TitleStructure of M. tuberculosis MazF-mt1 (Rv2801c) in complex with RNA
Components
  • Endoribonuclease MazF9
  • RNA (5'-R(*CP*AP*UP*C)-D(P*U)-R(P*AP*CP*CP*UP*GP*A)-3')
Keywordshydrolase/rna / toxin-antitoxin system / MazF / hydrolase-rna complex
Function / homology
Function and homology information


symbiont-mediated perturbation of host process / negative regulation of growth / rRNA catabolic process / mRNA catabolic process / 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
RNA / RNA (> 10) / Endoribonuclease MazF9
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.976 Å
AuthorsYen, T.J. / Brennan, R.G.
CitationJournal: To Be Published
Title: Structure of M. tuberculosis MazF-mt1 (Rv2801c) in complex with RNA
Authors: Yen, T.J. / Brennan, R.G.
History
DepositionJan 13, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Endoribonuclease MazF9
B: Endoribonuclease MazF9
C: RNA (5'-R(*CP*AP*UP*C)-D(P*U)-R(P*AP*CP*CP*UP*GP*A)-3')


Theoretical massNumber of molelcules
Total (without water)29,3653
Polymers29,3653
Non-polymers00
Water2,702150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3990 Å2
ΔGint-12 kcal/mol
Surface area10630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.799, 68.542, 80.162
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Endoribonuclease MazF9 / Toxin MazF9 / mRNA interferase MazF-mt1


Mass: 12976.825 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: mazF9, mazF-mt1, Rv2801c / Production host: Escherichia coli (E. coli)
References: UniProt: P71650, Hydrolases; Acting on ester bonds
#2: RNA chain RNA (5'-R(*CP*AP*UP*C)-D(P*U)-R(P*AP*CP*CP*UP*GP*A)-3')


Mass: 3411.091 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Production host: Escherichia coli (E. coli)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / 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: 1.81 Å3/Da / Density % sol: 32.23 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 25% PEG1500, 0.1 M MMT buffer

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.98→50 Å / Num. obs: 15533 / % possible obs: 100 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.04 / Rrim(I) all: 0.097 / Χ2: 1.13 / Net I/av σ(I): 21.931 / Net I/σ(I): 7.5 / Num. measured all: 90794
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.98-2.015.40.4727740.9480.2220.5230.85299.5
2.01-2.055.60.4227340.9390.1940.4660.87699.9
2.05-2.095.80.3967560.9630.180.4360.849100
2.09-2.135.90.3397720.9620.1520.3720.889100
2.13-2.1860.287740.9780.1260.3080.928100
2.18-2.2360.2667390.9730.1190.2920.939100
2.23-2.2960.2357840.9740.1050.2571100
2.29-2.3560.2117530.9810.0950.2321.002100
2.35-2.4260.27690.9840.0890.220.987100
2.42-2.495.90.1737580.9870.0780.190.978100
2.49-2.5860.1627730.9850.0730.1781.038100
2.58-2.695.90.137650.9910.0580.1431.076100
2.69-2.815.90.1257830.990.0560.1381.123100
2.81-2.965.90.0987750.9940.0440.1071.184100
2.96-3.145.90.0867700.9950.0390.0941.318100
3.14-3.395.90.0797810.9950.0360.0871.601100
3.39-3.735.90.0687910.9970.0310.0741.931100
3.73-4.265.80.057970.9970.0230.0561.577100
4.26-5.375.80.0398060.9990.0180.0431.26100
5.37-505.40.0348790.9990.0160.0381.10299.9

-
Processing

Software
NameVersionClassification
PHENIXrefinement
HKL-2000data scaling
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: B. subtilis MazF

Resolution: 1.976→34.923 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2304 1548 10 %
Rwork0.2061 13930 -
obs0.2085 15478 99.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 60.96 Å2 / Biso mean: 25.3823 Å2 / Biso min: 11.76 Å2
Refinement stepCycle: final / Resolution: 1.976→34.923 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1751 82 0 150 1983
Biso mean---31.69 -
Num. residues----234
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031857
X-RAY DIFFRACTIONf_angle_d0.622534
X-RAY DIFFRACTIONf_chiral_restr0.023314
X-RAY DIFFRACTIONf_plane_restr0.004318
X-RAY DIFFRACTIONf_dihedral_angle_d13.192712
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9763-2.04010.27071310.23161180131193
2.0401-2.1130.27631380.221612391377100
2.113-2.19760.26241370.211112441381100
2.1976-2.29760.20921410.209512651406100
2.2976-2.41870.29931380.203512371375100
2.4187-2.57020.22641410.220612641405100
2.5702-2.76860.24251410.211512701411100
2.7686-3.0470.24011400.217512651405100
3.047-3.48760.22761430.215712871430100
3.4876-4.39260.20411450.175912991444100
4.3926-34.92880.21061530.206513801533100

+
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