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

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4uqz
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
ACETATE ION / 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: 1.599 Å
AuthorsForster, A. / Planamente, S. / Manoli, E. / Lossi, N.S. / Freemont, P.S. / Filloux, A.
CitationJournal: RNA / 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 / 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: HSIE1
B: HSIB1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2503
Polymers47,1912
Non-polymers591
Water5,657314
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3050 Å2
ΔGint-9.1 kcal/mol
Surface area12750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.112, 67.323, 94.025
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein HSIE1


Mass: 28383.232 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 HSIB1


Mass: 18807.598 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: PROTEIN DEGRADED DURING PURIFICATION / Source: (gene. exp.) PSEUDOMONAS AERUGINOSA PAO1 (bacteria) / Production host: ESCHERICHIA COLI B (bacteria) / Strain (production host): B384 / References: UniProt: Q9I749
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 314 / 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: 2.48 Å3/Da / Density % sol: 50.44 % / Description: NONE
Crystal growpH: 8 / Details: 100 MM TRIS(PH 8.0), 24% PEG6000, 0.2 M CACL2

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.98
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 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→54.7 Å / Num. obs: 43478 / % possible obs: 98.1 % / Observed criterion σ(I): 1.5 / Redundancy: 5 % / Biso Wilson estimate: 18.52 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 11.4
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.7 / % possible all: 96

-
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: 1.599→41.209 Å / SU ML: 0.18 / σ(F): 0.03 / Phase error: 25.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2206 4003 5 %
Rwork0.1876 --
obs0.1893 41994 94.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.44 Å2
Refinement stepCycle: LAST / Resolution: 1.599→41.209 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2172 0 4 314 2490
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122238
X-RAY DIFFRACTIONf_angle_d1.4143051
X-RAY DIFFRACTIONf_dihedral_angle_d13.614819
X-RAY DIFFRACTIONf_chiral_restr0.066348
X-RAY DIFFRACTIONf_plane_restr0.007405
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5994-1.61820.29111110.26322278X-RAY DIFFRACTION82
1.6182-1.63790.30931360.25472415X-RAY DIFFRACTION86
1.6379-1.65870.29171250.2252413X-RAY DIFFRACTION88
1.6587-1.68050.30761060.22772469X-RAY DIFFRACTION88
1.6805-1.70350.2481410.22432506X-RAY DIFFRACTION91
1.7035-1.72790.20911360.21332514X-RAY DIFFRACTION91
1.7279-1.75370.26971450.21572624X-RAY DIFFRACTION95
1.7537-1.78110.25591390.21132676X-RAY DIFFRACTION95
1.7811-1.81030.30731110.20312743X-RAY DIFFRACTION97
1.8103-1.84150.27761750.22312563X-RAY DIFFRACTION96
1.8415-1.8750.22071190.23862586X-RAY DIFFRACTION92
1.875-1.9110.29911370.30652402X-RAY DIFFRACTION87
1.911-1.950.40071470.34792543X-RAY DIFFRACTION93
1.95-1.99240.21381730.21042594X-RAY DIFFRACTION95
1.9924-2.03880.25391300.18452721X-RAY DIFFRACTION98
2.0388-2.08980.20051660.17412692X-RAY DIFFRACTION98
2.0898-2.14630.22191680.17592709X-RAY DIFFRACTION99
2.1463-2.20940.29931140.1942576X-RAY DIFFRACTION93
2.2094-2.28070.30041400.27442598X-RAY DIFFRACTION94
2.2807-2.36220.22541090.19182686X-RAY DIFFRACTION95
2.3622-2.45680.18321270.17642734X-RAY DIFFRACTION99
2.4568-2.56860.19381480.17742727X-RAY DIFFRACTION99
2.5686-2.7040.21661300.18132735X-RAY DIFFRACTION98
2.704-2.87340.23781190.18982719X-RAY DIFFRACTION98
2.8734-3.09510.2071320.17812681X-RAY DIFFRACTION96
3.0951-3.40650.20191340.16922762X-RAY DIFFRACTION100
3.4065-3.89910.18461300.14922776X-RAY DIFFRACTION100
3.8991-4.91120.15191650.13372733X-RAY DIFFRACTION100
4.9112-41.22240.19431900.15462708X-RAY DIFFRACTION99
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)
12.0262-0.693-0.58792.66720.28743.8246-0.05270.31870.237-0.4604-0.0046-0.0762-0.4601-0.00640.04230.2647-0.0469-0.05820.21550.02460.1464-5.31349.0216-48.0314
22.2784-0.649-2.62170.8360.34855.7424-0.03630.1803-0.13490.0472-0.01330.08750.0324-0.3030.05590.1347-0.0317-0.02380.13590.00430.175-11.03210.2565-20.9051
30.60860.2369-0.05992.0120.0052.4018-0.0144-0.0433-0.01270.18250.009-0.1079-0.05560.15930.00440.0852-0.0117-0.02520.10170.00310.1287-1.29319.6604-21.8002
47.175-0.6809-0.647.5149-2.0720.66760.2202-0.4140.75331.14540.40940.2968-1.1294-0.7375-0.6170.39810.09160.02730.2628-0.02050.2531-7.036613.9859-8.1437
53.0025-0.3307-4.90426.93950.30758.1658-0.2677-0.0837-0.13470.6420.08530.28020.01970.09020.20880.28070.0203-0.02590.2001-0.00580.2463-6.495222.8942-21.9834
62.0303-0.501-2.28070.95362.4026.6375-0.12840.44140.0491-0.35370.5678-0.4682-0.5710.5947-0.41930.3326-0.12450.04010.2883-0.03370.25574.73413.2928-41.2725
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 156 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 157 THROUGH 287 )
4X-RAY DIFFRACTION4CHAIN 'B' AND (RESID 8 THROUGH 12 )
5X-RAY DIFFRACTION5CHAIN 'B' AND (RESID 13 THROUGH 22 )
6X-RAY DIFFRACTION6CHAIN 'B' AND (RESID 23 THROUGH 31 )

+
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