[English] 日本語
Yorodumi
- PDB-6hs6: C-terminal domain of the TssA component of the type VI secretion ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6hs6
TitleC-terminal domain of the TssA component of the type VI secretion system from Burkholderia cenocepacia
ComponentsType VI secretion protein ImpA
KeywordsTRANSPORT PROTEIN / alpha-helical protein / type VI secretion system component / TssA
Function / homologyType VI secretion system protein TssA-like / ImpA, N-terminal / ImpA, N-terminal, type VI secretion system / metal ion binding / Type VI secretion protein ImpA
Function and homology information
Biological speciesBurkholderia cenocepacia H111 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.08 Å
AuthorsDix, S.R. / Owen, H.J. / Sun, R. / Ahmad, A. / Shastri, S. / Spiewak, H.L. / Mosby, D.J. / Harris, M.J. / Batters, S.L. / Brooker, T.A. ...Dix, S.R. / Owen, H.J. / Sun, R. / Ahmad, A. / Shastri, S. / Spiewak, H.L. / Mosby, D.J. / Harris, M.J. / Batters, S.L. / Brooker, T.A. / Tzokov, S.B. / Sedelnikova, S.E. / Baker, P.J. / Bullough, P.A. / Rice, D.W. / Thomas, M.S.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/J014443/1 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/F016840/1 United Kingdom
Higher Education Funding Council for EnglandR/151699 United Kingdom
CitationJournal: Nat Commun / Year: 2018
Title: Structural insights into the function of type VI secretion system TssA subunits.
Authors: Dix, S.R. / Owen, H.J. / Sun, R. / Ahmad, A. / Shastri, S. / Spiewak, H.L. / Mosby, D.J. / Harris, M.J. / Batters, S.L. / Brooker, T.A. / Tzokov, S.B. / Sedelnikova, S.E. / Baker, P.J. / ...Authors: Dix, S.R. / Owen, H.J. / Sun, R. / Ahmad, A. / Shastri, S. / Spiewak, H.L. / Mosby, D.J. / Harris, M.J. / Batters, S.L. / Brooker, T.A. / Tzokov, S.B. / Sedelnikova, S.E. / Baker, P.J. / Bullough, P.A. / Rice, D.W. / Thomas, M.S.
History
DepositionSep 28, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 21, 2018Provider: repository / Type: Initial release
Revision 1.1May 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: Type VI secretion protein ImpA
C: Type VI secretion protein ImpA
H: Type VI secretion protein ImpA
G: Type VI secretion protein ImpA
F: Type VI secretion protein ImpA
E: Type VI secretion protein ImpA
D: Type VI secretion protein ImpA
B: Type VI secretion protein ImpA


Theoretical massNumber of molelcules
Total (without water)68,7418
Polymers68,7418
Non-polymers00
Water00
1
A: Type VI secretion protein ImpA
C: Type VI secretion protein ImpA
H: Type VI secretion protein ImpA
G: Type VI secretion protein ImpA
F: Type VI secretion protein ImpA
E: Type VI secretion protein ImpA
D: Type VI secretion protein ImpA
B: Type VI secretion protein ImpA

A: Type VI secretion protein ImpA
C: Type VI secretion protein ImpA
H: Type VI secretion protein ImpA
G: Type VI secretion protein ImpA
F: Type VI secretion protein ImpA
E: Type VI secretion protein ImpA
D: Type VI secretion protein ImpA
B: Type VI secretion protein ImpA

A: Type VI secretion protein ImpA
C: Type VI secretion protein ImpA
H: Type VI secretion protein ImpA
G: Type VI secretion protein ImpA
F: Type VI secretion protein ImpA
E: Type VI secretion protein ImpA
D: Type VI secretion protein ImpA
B: Type VI secretion protein ImpA

A: Type VI secretion protein ImpA
C: Type VI secretion protein ImpA
H: Type VI secretion protein ImpA
G: Type VI secretion protein ImpA
F: Type VI secretion protein ImpA
E: Type VI secretion protein ImpA
D: Type VI secretion protein ImpA
B: Type VI secretion protein ImpA


Theoretical massNumber of molelcules
Total (without water)274,96632
Polymers274,96632
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_655-x+1,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area86520 Å2
ΔGint-622 kcal/mol
Surface area94560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.330, 201.700, 263.660
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

-
Components

#1: Protein
Type VI secretion protein ImpA / TssA


Mass: 8592.672 Da / Num. of mol.: 8 / Fragment: UNP residues 303-373
Source method: isolated from a genetically manipulated source
Details: Purification by maltose binding protein cleaved after IEGRRemaining tag residues ISHM - 299-302Construct comprises residues 303-373 of full-length protein (total 373 residues)
Source: (gene. exp.) Burkholderia cenocepacia H111 (bacteria)
Gene: I35_RS01755 / Plasmid: pMAL-c5x / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): NEB Express / References: UniProt: A0A1V2W6E8

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 4.48 Å3/Da / Density % sol: 72.55 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: 0.1M sodium chloride, 0.1M Tris pH8.0, 15% (v/v) ethanol, 5% (v/v) MPD

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 1.70001 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 31, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.70001 Å / Relative weight: 1
ReflectionResolution: 3.08→41.49 Å / Num. obs: 23602 / % possible obs: 99.9 % / Redundancy: 12.6 % / Rmerge(I) obs: 0.131 / Rpim(I) all: 0.04 / Net I/σ(I): 17.5
Reflection shellResolution: 3.08→3.16 Å / Redundancy: 11.9 % / Rmerge(I) obs: 0.786 / Mean I/σ(I) obs: 3.7 / Num. unique obs: 1709 / Rpim(I) all: 0.251 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
xia2data reduction
xia2data scaling
SHELXCDphasing
RefinementMethod to determine structure: SAD / Resolution: 3.08→41.49 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.907 / SU B: 13.567 / SU ML: 0.238 / Cross valid method: THROUGHOUT / ESU R: 0.596 / ESU R Free: 0.337 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24245 1215 5.1 %RANDOM
Rwork0.19826 ---
obs0.20048 22387 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 69.705 Å2
Baniso -1Baniso -2Baniso -3
1-4.1 Å20 Å20 Å2
2---2.82 Å20 Å2
3----1.28 Å2
Refinement stepCycle: 1 / Resolution: 3.08→41.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4401 0 0 0 4401
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0194503
X-RAY DIFFRACTIONr_bond_other_d0.0020.024340
X-RAY DIFFRACTIONr_angle_refined_deg1.6211.9416107
X-RAY DIFFRACTIONr_angle_other_deg0.98339921
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.1325540
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.53822.902224
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.28115761
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.8611547
X-RAY DIFFRACTIONr_chiral_restr0.0870.2661
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215066
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021079
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_it4.5556.6582184
X-RAY DIFFRACTIONr_mcbond_other4.5426.6572183
X-RAY DIFFRACTIONr_mcangle_it7.329.9642716
X-RAY DIFFRACTIONr_mcangle_other7.329.9662717
X-RAY DIFFRACTIONr_scbond_it4.7637.1942319
X-RAY DIFFRACTIONr_scbond_other4.7627.1962320
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.75210.5393391
X-RAY DIFFRACTIONr_long_range_B_refined10.37251.0934926
X-RAY DIFFRACTIONr_long_range_B_other10.37251.1064927
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.08→3.16 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.387 75 -
Rwork0.283 1621 -
obs--99.94 %

+
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