[English] 日本語
Yorodumi
- PDB-4v3i: Crystal Structure of TssL from Vibrio cholerae. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4v3i
TitleCrystal Structure of TssL from Vibrio cholerae.
Components(VCA0115) x 2
KeywordsUNKNOWN FUNCTION / T6SS / VIBRIO CHOLERAE / TSSL / VCA0115
Function / homologyType IV / VI secretion system, DotU / Type IV / VI secretion system, DotU / Type IV / VI secretion system, DotU superfamily / Type VI secretion system protein DotU / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha / membrane / Type IV / VI secretion system DotU domain-containing protein
Function and homology information
Biological speciesVIBRIO CHOLERAE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.499 Å
AuthorsJeong, J.H. / Kim, Y.G.
CitationJournal: J. Microbiol. / Year: 2015
Title: Crystal structure of the bacterial type VI secretion system component TssL from Vibrio cholerae.
Authors: Chang, J.H. / Kim, Y.G.
History
DepositionOct 19, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 17, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 21, 2015Group: Database references
Revision 1.2May 10, 2017Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: VCA0115
B: VCA0115
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4063
Polymers30,3132
Non-polymers921
Water1,20767
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area820 Å2
ΔGint-3.6 kcal/mol
Surface area8510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.361, 78.361, 49.456
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

-
Components

#1: Protein VCA0115


Mass: 29711.797 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) VIBRIO CHOLERAE (bacteria) / Plasmid: PET30A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9KN50
#2: Protein/peptide VCA0115


Mass: 601.673 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) VIBRIO CHOLERAE (bacteria) / Plasmid: PET30A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9KN50
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 2.58 Å3/Da / Density % sol: 52.3 % / Description: NONE
Crystal growpH: 6.4
Details: 1.8 M SODIUM CHLORIDE, 0.1 M SODIUM POTASSIUM PHOSPHATE PH 6.4

-
Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9795
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 4, 2013 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 27803 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 11 % / Biso Wilson estimate: 14.82 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 59
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 8.5 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 6.63 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3U66

3u66


Resolution: 1.499→27.979 Å / SU ML: 0.12 / σ(F): 1.58 / Phase error: 19.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1939 2012 7.2 %
Rwork0.1793 --
obs0.1804 27800 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.499→27.979 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1281 0 6 67 1354
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091312
X-RAY DIFFRACTIONf_angle_d1.1911769
X-RAY DIFFRACTIONf_dihedral_angle_d14.623482
X-RAY DIFFRACTIONf_chiral_restr0.049194
X-RAY DIFFRACTIONf_plane_restr0.008224
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.499-1.53650.24711450.23271839X-RAY DIFFRACTION100
1.5365-1.5780.2161420.20551824X-RAY DIFFRACTION100
1.578-1.62450.23791350.19511844X-RAY DIFFRACTION100
1.6245-1.67690.22341420.17861844X-RAY DIFFRACTION100
1.6769-1.73680.18311460.1751819X-RAY DIFFRACTION100
1.7368-1.80630.17631440.17091855X-RAY DIFFRACTION100
1.8063-1.88850.21151430.17481829X-RAY DIFFRACTION100
1.8885-1.98810.21781470.17881809X-RAY DIFFRACTION100
1.9881-2.11260.20971420.16521857X-RAY DIFFRACTION100
2.1126-2.27560.1781450.16881842X-RAY DIFFRACTION100
2.2756-2.50450.19221440.17951857X-RAY DIFFRACTION100
2.5045-2.86660.19461410.18521860X-RAY DIFFRACTION100
2.8666-3.61040.17821480.17881857X-RAY DIFFRACTION100
3.6104-27.98410.18561480.17621852X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: 4.8855 Å / Origin y: 27.9566 Å / Origin z: -2.366 Å
111213212223313233
T0.0725 Å2-0.0092 Å20.0295 Å2-0.0809 Å20.0073 Å2--0.1153 Å2
L2.5907 °2-0.7914 °2-0.1423 °2-2.0716 °20.4406 °2--1.2541 °2
S-0.019 Å °-0.0243 Å °-0.1254 Å °0.0048 Å °0.0396 Å °-0.0263 Å °0.0662 Å °0.099 Å °-0.0149 Å °
Refinement TLS groupSelection details: ALL

+
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