[English] 日本語
Yorodumi
- PDB-6grk: Structure of the soluble AhlB of the tripartite alpha-pore formin... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6grk
TitleStructure of the soluble AhlB of the tripartite alpha-pore forming toxin, AHL, from Aeromonas hydrophila.
ComponentsAhlB
KeywordsTOXIN / Tripartite pore-forming toxin
Function / homology
Function and homology information


membrane => GO:0016020 / membrane
Similarity search - Function
Hemolysin BL-binding component / Bacillus haemolytic enterotoxin (HBL) / : / Hemolysin E; Chain: A; / Hemolysin E; Chain: A; - #10 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Alpha-helical pore-forming toxin family protein / Alpha-helical pore-forming toxin family protein
Similarity search - Component
Biological speciesAeromonas hydrophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 Å
AuthorsChurchill-Angus, A.M. / Wilson, J.S. / Baker, P.J.
CitationJournal: Nat Commun / Year: 2019
Title: Identification and structural analysis of the tripartite alpha-pore forming toxin of Aeromonas hydrophila.
Authors: Wilson, J.S. / Churchill-Angus, A.M. / Davies, S.P. / Sedelnikova, S.E. / Tzokov, S.B. / Rafferty, J.B. / Bullough, P.A. / Bisson, C. / Baker, P.J.
History
DepositionJun 11, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 3, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2019Group: Data collection / Database references
Category: citation / database_PDB_rev ...citation / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jul 17, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: AhlB
I: AhlB
B: AhlB


Theoretical massNumber of molelcules
Total (without water)116,2043
Polymers116,2043
Non-polymers00
Water1,820101
1
A: AhlB


Theoretical massNumber of molelcules
Total (without water)38,7351
Polymers38,7351
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
I: AhlB


Theoretical massNumber of molelcules
Total (without water)38,7351
Polymers38,7351
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: AhlB


Theoretical massNumber of molelcules
Total (without water)38,7351
Polymers38,7351
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)133.470, 79.810, 111.010
Angle α, β, γ (deg.)90.00, 90.22, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11I-410-

HOH

-
Components

#1: Protein AhlB


Mass: 38734.520 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aeromonas hydrophila (bacteria) / Gene: A9R12_16795 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A081US78, UniProt: A0A454GEH4*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / 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: 2.54 Å3/Da / Density % sol: 51.65 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.2 M potassium thiocyanate, 0.1 M bis-tris propane pH 6.5, and 20 % PEG3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 11, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.895
11-1/2H+3/2K, -1/2H-1/2K, L20.105
ReflectionResolution: 2.33→58.34 Å / Num. obs: 49043 / % possible obs: 98.1 % / Redundancy: 3.3 % / Net I/σ(I): 0.791
Reflection shellResolution: 2.33→2.39 Å

-
Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.33→58.41 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.911 / SU B: 8.863 / SU ML: 0.201 / Cross valid method: THROUGHOUT / ESU R: 0.384 / ESU R Free: 0.249 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25361 2504 5.1 %RANDOM
Rwork0.22232 ---
obs0.22391 46538 98.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.943 Å2
Baniso -1Baniso -2Baniso -3
1--1.57 Å20 Å21.64 Å2
2--1.26 Å20 Å2
3---0.3 Å2
Refinement stepCycle: 1 / Resolution: 2.33→58.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7774 0 0 101 7875
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0147860
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177271
X-RAY DIFFRACTIONr_angle_refined_deg1.4081.63610714
X-RAY DIFFRACTIONr_angle_other_deg0.9671.63716957
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.59251051
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.94625.988344
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.384151301
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0871521
X-RAY DIFFRACTIONr_chiral_restr0.0720.21138
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.028940
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021288
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.7084.8614216
X-RAY DIFFRACTIONr_mcbond_other3.7054.864215
X-RAY DIFFRACTIONr_mcangle_it5.4967.2825263
X-RAY DIFFRACTIONr_mcangle_other5.4967.2835264
X-RAY DIFFRACTIONr_scbond_it3.7135.1013644
X-RAY DIFFRACTIONr_scbond_other3.7125.1023645
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.6527.5355452
X-RAY DIFFRACTIONr_long_range_B_refined7.70559.8929175
X-RAY DIFFRACTIONr_long_range_B_other7.70459.9039169
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.33→2.391 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 195 -
Rwork0.309 3462 -
obs--99.75 %

+
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