[English] 日本語
Yorodumi
- PDB-5ixl: Structure of P. vulgaris HigB toxin Y91A variant -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ixl
TitleStructure of P. vulgaris HigB toxin Y91A variant
ComponentsEndoribonuclease HigB
KeywordsHYDROLASE / bacterial toxins / biofilms / cell metabolism / energy metabolism / microbial pathogenesis / stress response / stringent response / translation control
Function / homology
Function and homology information


plasmid maintenance / RNA catabolic process / translation repressor activity / RNA endonuclease activity / negative regulation of cell growth / ribosome binding / negative regulation of translation / Hydrolases; Acting on ester bonds / negative regulation of cell population proliferation / mRNA binding
Similarity search - Function
Toxin HigB-1 / RelE-like toxin of type II toxin-antitoxin system HigB / RelE-like / YaeB-like fold / Toxin-antitoxin system, RelE/ParE toxin domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Endoribonuclease HigB
Similarity search - Component
Biological speciesProteus vulgaris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsSchureck, M.A. / Repack, A.A. / Miles, S.J. / Marquez, J. / Dunham, C.M.
CitationJournal: Nucleic Acids Res. / Year: 2016
Title: Mechanism of endonuclease cleavage by the HigB toxin.
Authors: Schureck, M.A. / Repack, A. / Miles, S.J. / Marquez, J. / Dunham, C.M.
History
DepositionMar 23, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2016Group: Database references
Revision 1.2Sep 27, 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 / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Endoribonuclease HigB
B: Endoribonuclease HigB
C: Endoribonuclease HigB
D: Endoribonuclease HigB
E: Endoribonuclease HigB
F: Endoribonuclease HigB
G: Endoribonuclease HigB
H: Endoribonuclease HigB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,39620
Polymers108,9708
Non-polymers42512
Water10,953608
1
A: Endoribonuclease HigB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6572
Polymers13,6211
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Endoribonuclease HigB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7284
Polymers13,6211
Non-polymers1063
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Endoribonuclease HigB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6572
Polymers13,6211
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Endoribonuclease HigB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6923
Polymers13,6211
Non-polymers712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Endoribonuclease HigB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6572
Polymers13,6211
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Endoribonuclease HigB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6572
Polymers13,6211
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: Endoribonuclease HigB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6572
Polymers13,6211
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: Endoribonuclease HigB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6923
Polymers13,6211
Non-polymers712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)113.340, 64.030, 94.080
Angle α, β, γ (deg.)90.00, 98.14, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein
Endoribonuclease HigB / Host inhibition of growth protein B / Killer protein / Toxin HigB / mRNA interferase HigB


Mass: 13621.312 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Proteus vulgaris (bacteria) / Gene: higB / Plasmid: pBAD/Myc-HisA / Production host: Escherichia coli BW25113 (bacteria)
References: UniProt: Q7A225, Hydrolases; Acting on ester bonds
#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 608 / 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: 1.55 Å3/Da / Density % sol: 20.68 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 40% (w/v) polyethylene glycol monomethylether 2,000 and 0.15 M KBr

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Feb 15, 2015
RadiationMonochromator: Cryogenically-cooled Si-220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.55→100 Å / Num. obs: 87109 / % possible obs: 85.7 % / Redundancy: 2.6 % / Net I/σ(I): 12
Reflection shellResolution: 1.55→1.6 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 2.4 / % possible all: 89.9

-
Processing

Software
NameVersionClassification
PHENIX1.8.3_1479refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PX8

4px8


Resolution: 1.55→37.004 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.55
RfactorNum. reflection% reflectionSelection details
Rfree0.2152 1700 1.95 %Random selection
Rwork0.1683 ---
obs0.1692 87109 90.03 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.55→37.004 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6202 0 12 608 6822
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0136389
X-RAY DIFFRACTIONf_angle_d1.3338626
X-RAY DIFFRACTIONf_dihedral_angle_d12.882378
X-RAY DIFFRACTIONf_chiral_restr0.065917
X-RAY DIFFRACTIONf_plane_restr0.0061118
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.59560.27441520.21477326X-RAY DIFFRACTION93
1.5956-1.64710.3121460.20727356X-RAY DIFFRACTION93
1.6471-1.7060.24761460.19397325X-RAY DIFFRACTION93
1.706-1.77430.24211440.1787314X-RAY DIFFRACTION93
1.7743-1.8550.23651370.17357285X-RAY DIFFRACTION92
1.855-1.95280.24081420.16747233X-RAY DIFFRACTION92
1.9528-2.07510.19641410.15917171X-RAY DIFFRACTION91
2.0751-2.23530.21091490.15627162X-RAY DIFFRACTION90
2.2353-2.46020.22341390.1617050X-RAY DIFFRACTION89
2.4602-2.81610.22041360.16986966X-RAY DIFFRACTION88
2.8161-3.54760.17861360.16586798X-RAY DIFFRACTION85
3.5476-37.0140.19991320.16156423X-RAY DIFFRACTION79

+
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