[English] 日本語
Yorodumi
- PDB-5hk0: Crystal structure of M. tuberculosis MazF-mt3 (Rv1991c) in comple... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5hk0
TitleCrystal structure of M. tuberculosis MazF-mt3 (Rv1991c) in complex with RNA
Components
  • Endoribonuclease MazF6
  • RNA (5'-R(*AP*GP*UP*C)-D(P*U)-R(P*CP*CP*UP*UP*UP*C)-3')
Keywordshydrolase/rna / toxin-antitoxin system / MazF / hydrolase-rna complex
Function / homology
Function and homology information


symbiont-mediated perturbation of host process / positive regulation of growth / negative regulation of growth / rRNA catabolic process / Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / mRNA catabolic process / RNA nuclease activity / RNA endonuclease activity / DNA binding / extracellular region
Similarity search - Function
SH3 type barrels. - #110 / mRNA interferase PemK-like / PemK-like, MazF-like toxin of type II toxin-antitoxin system / Plasmid maintenance toxin/Cell growth inhibitor / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
RNA / RNA (> 10) / Endoribonuclease MazF6
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsYen, T.J. / Brennan, R.G.
CitationJournal: To Be Published
Title: Crystal structure of M. tuberculosis MazF-mt3 (Rv1991c) 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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_oper_list.symmetry_operation
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 MazF6
B: Endoribonuclease MazF6
C: Endoribonuclease MazF6
D: Endoribonuclease MazF6
E: RNA (5'-R(*AP*GP*UP*C)-D(P*U)-R(P*CP*CP*UP*UP*UP*C)-3')
F: RNA (5'-R(*AP*GP*UP*C)-D(P*U)-R(P*CP*CP*UP*UP*UP*C)-3')


Theoretical massNumber of molelcules
Total (without water)55,8316
Polymers55,8316
Non-polymers00
Water3,099172
1
A: Endoribonuclease MazF6
B: Endoribonuclease MazF6
E: RNA (5'-R(*AP*GP*UP*C)-D(P*U)-R(P*CP*CP*UP*UP*UP*C)-3')


Theoretical massNumber of molelcules
Total (without water)27,9153
Polymers27,9153
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Endoribonuclease MazF6
D: Endoribonuclease MazF6
F: RNA (5'-R(*AP*GP*UP*C)-D(P*U)-R(P*CP*CP*UP*UP*UP*C)-3')


Theoretical massNumber of molelcules
Total (without water)27,9153
Polymers27,9153
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.338, 68.338, 88.364
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32

-
Components

#1: Protein
Endoribonuclease MazF6 / Toxin MazF6 / mRNA interferase MazF-mt3


Mass: 12275.140 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: mazF6, mazF-mt3, Rv1991c, MTCY39.28 / Production host: Escherichia coli (E. coli)
References: UniProt: P9WII3, Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters
#2: RNA chain RNA (5'-R(*AP*GP*UP*C)-D(P*U)-R(P*CP*CP*UP*UP*UP*C)-3')


Mass: 3365.011 Da / Num. of mol.: 2
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.: 172 / 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: 2.13 Å3/Da / Density % sol: 42.35 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4 / Details: 0.8 M Ammonium sulfate, 0.1 M sodium citrate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-X / Wavelength: 1.5 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: May 8, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5 Å / Relative weight: 1
Reflection twinOperator: h,-h-k,-l / Fraction: 0.5
ReflectionResolution: 2.25→50 Å / Num. obs: 21890 / % possible obs: 99.6 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.054 / Χ2: 1.019 / Net I/av σ(I): 19.525 / Net I/σ(I): 12.4 / Num. measured all: 61859
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.25-2.292.50.4310850.87895.9
2.29-2.332.70.4210770.8599.3
2.33-2.382.70.38411050.86299.6
2.38-2.422.80.32911060.86199.9
2.42-2.482.80.26910690.91100
2.48-2.532.80.24811170.923100
2.53-2.62.80.28910901.44199.9
2.6-2.672.80.21410940.998100
2.67-2.752.80.17310940.894100
2.75-2.832.80.13811180.967100
2.83-2.942.80.10810681.015100
2.94-3.052.90.08410991.074100
3.05-3.192.90.07111070.979100
3.19-3.362.90.05610881.067100
3.36-3.572.90.04310961.087100
3.57-3.852.90.0411021.025100
3.85-4.232.90.03111001.151100
4.23-4.852.90.02610891.16999.9
4.85-6.12.90.02710911.09399.6
6.1-502.90.02310951.06298.8

-
Processing

Software
NameVersionClassification
PHENIXrefinement
HKL-3000data scaling
PDB_EXTRACT3.15data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: B. subtilis MazF

Resolution: 2.25→49.173 Å / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 28.31 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2568 1996 9.12 %
Rwork0.2121 19847 -
obs0.2156 21877 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 105.13 Å2 / Biso mean: 40.1914 Å2 / Biso min: 19.16 Å2
Refinement stepCycle: final / Resolution: 2.25→49.173 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3248 138 39 172 3597
Biso mean--44.34 40.15 -
Num. residues----431
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023444
X-RAY DIFFRACTIONf_angle_d0.7214729
X-RAY DIFFRACTIONf_chiral_restr0.027609
X-RAY DIFFRACTIONf_plane_restr0.004576
X-RAY DIFFRACTIONf_dihedral_angle_d14.5711284
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2513-2.30760.36351540.28341397155187
2.3076-2.370.39361420.28951437157991
2.37-2.43970.32681410.27981397153891
2.4397-2.51850.32691340.25681431156591
2.5185-2.60840.33931400.27041428156891
2.6084-2.71280.3381440.25771399154391
2.7128-2.83620.371380.2451439157791
2.8362-2.98570.28431480.23811387153590
2.9857-3.17260.27551310.22721437156892
3.1726-3.41740.26691400.20251453159391
3.4174-3.76090.25641480.19291387153590
3.7609-4.30420.21061390.17261430156991
4.3042-5.41940.16531480.16191402155090
5.4194-34.17290.2341440.20961423156791

+
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