[English] 日本語
Yorodumi
- PDB-4uqy: Coevolution of the ATPase ClpV, the TssB-TssC Sheath and the Acce... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4uqy
TitleCoevolution of the ATPase ClpV, the TssB-TssC Sheath and the Accessory HsiE Protein Distinguishes Two Type VI Secretion Classes
Components
  • HSIB1
  • HSIE1
KeywordsPROTEIN TRANSPORT / SECRETION / SHEATH / DISASSEMBLY / REGULATION / BACTERIAL
Function / homology
Function and homology information


Type VI secretion system accessory component TagJ / ImpE protein / Type VI secretion system sheath protein TssB1 / Type VI secretion system, VipA, VC_A0107 or Hcp2 / Tetratricopeptide repeat / Tetratricopeptide repeat domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Mainly Alpha
Similarity search - Domain/homology
Type VI secretion system accessory component TagJ / Type VI secretion system sheath protein TssB1
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsForster, A. / Planamente, S. / Manoli, E. / Lossi, N.S. / Freemont, P.S. / Filloux, A.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Coevolution of the ATPase Clpv, the Sheath Proteins Tssb and Tssc and the Accessory Protein Tagj/Hsie1 Distinguishes Type Vi Secretion Classes.
Authors: Forster, A. / Planamente, S. / Manoli, E. / Lossi, N.S. / Freemont, P.S. / Filloux, A.
History
DepositionJun 25, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 22, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 3, 2014Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HSIE1
B: HSIB1


Theoretical massNumber of molelcules
Total (without water)30,9052
Polymers30,9052
Non-polymers00
Water3,549197
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1500 Å2
ΔGint-4.9 kcal/mol
Surface area12340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.220, 63.970, 94.540
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein HSIE1


Mass: 28665.506 Da / Num. of mol.: 1 / Fragment: RESIDUES 21-281
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA PAO1 (bacteria) / Production host: ESCHERICHIA COLI B (bacteria) / Strain (production host): B834 / References: UniProt: Q9I746
#2: Protein/peptide HSIB1


Mass: 2239.558 Da / Num. of mol.: 1 / Fragment: N TERMINUS, RESIDUES 1-20 / Source method: obtained synthetically / Source: (synth.) PSEUDOMONAS AERUGINOSA PAO1 (bacteria) / References: UniProt: Q9I749
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / 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: 2.14 Å3/Da / Density % sol: 42.59 % / Description: NONE
Crystal growpH: 6.5
Details: 50 MM MES (PH 6.5) 100 MM AMMONIUM ACETATE 10% GLYCEROL 28% PEG 8000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.98
DetectorType: ADSC ADSC CCD / Detector: CCD / Date: Feb 3, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.6→53 Å / Num. obs: 36309 / % possible obs: 99.8 % / Observed criterion σ(I): 1.5 / Redundancy: 3.2 % / Biso Wilson estimate: 18.08 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 10.7
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 2.2 / % possible all: 98.5

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ZBP

1zbp


Resolution: 1.6→30.298 Å / SU ML: 0.15 / σ(F): 1.35 / Phase error: 20.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2051 1806 5 %
Rwork0.1766 --
obs0.178 35818 96.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.74 Å2
Refinement stepCycle: LAST / Resolution: 1.6→30.298 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2079 0 0 197 2276
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062182
X-RAY DIFFRACTIONf_angle_d1.0322983
X-RAY DIFFRACTIONf_dihedral_angle_d12.396810
X-RAY DIFFRACTIONf_chiral_restr0.041338
X-RAY DIFFRACTIONf_plane_restr0.005401
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.64330.29471450.28182536X-RAY DIFFRACTION97
1.6433-1.69160.27431330.23832599X-RAY DIFFRACTION97
1.6916-1.74620.22621450.2082580X-RAY DIFFRACTION97
1.7462-1.80860.23381420.20312597X-RAY DIFFRACTION97
1.8086-1.8810.24991400.18962571X-RAY DIFFRACTION97
1.881-1.96660.22161300.17572657X-RAY DIFFRACTION98
1.9666-2.07030.19981370.17132629X-RAY DIFFRACTION99
2.0703-2.20.21011530.16722654X-RAY DIFFRACTION99
2.2-2.36980.23311570.16992674X-RAY DIFFRACTION99
2.3698-2.60810.1931210.17512685X-RAY DIFFRACTION99
2.6081-2.98530.21281430.18122692X-RAY DIFFRACTION99
2.9853-3.760.17811340.16142718X-RAY DIFFRACTION98
3.76-30.30340.17531260.16522420X-RAY DIFFRACTION84
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.61630.01940.1911.84830.54962.11780.0329-0.4758-0.25910.58850.0633-0.14680.54840.0506-0.07160.47850.03110.00250.29120.05460.18317.9273-10.2540.6225
25.91970.18324.23912.46920.86528.0179-0.0662-0.31330.12340.11840.0996-0.046-0.426-0.0277-0.00750.25260.00670.05470.1814-0.00820.156719.03430.4143-12.4426
33.3470.57330.93511.02030.49395.2238-0.07520.1130.2028-0.11840.09670.066-0.1847-0.4747-0.0280.2420.0268-0.00840.13650.04050.165910.2489-0.4219-34.9037
41.03180.40260.10421.96310.00222.5045-0.00820.0098-0.09330.01650.0415-0.14270.08840.1184-0.02390.15710.02250.02490.0917-0.00460.163821.9963-10.4824-25.3179
51.58313.167-3.55516.4835-6.98768.0564-0.33330.3228-0.0241-0.64720.56180.12810.6808-0.6138-0.14020.2729-0.0304-0.00620.1575-0.01970.19714.3239-19.6604-32.0782
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 30 THROUGH 88 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 89 THROUGH 112 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 113 THROUGH 156 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 157 THROUGH 286 )
5X-RAY DIFFRACTION5CHAIN 'B' AND (RESID 8 THROUGH 20 )

+
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