[English] 日本語
Yorodumi
- PDB-6utu: Crystal structure of minor pseudopilin ternary complex of XcpVWX ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6utu
TitleCrystal structure of minor pseudopilin ternary complex of XcpVWX from the Type 2 secretion system of Pseudomonas aeruginosa in the P3 space group
Components
  • Type II secretion system protein I
  • Type II secretion system protein J
  • Type II secretion system protein K
KeywordsPROTEIN TRANSPORT / pseudopilus / minor pseduopilin
Function / homology
Function and homology information


protein secretion by the type II secretion system / type II protein secretion system complex / plasma membrane
Similarity search - Function
General secretion pathway protein K / GspK, central domain superfamily / : / : / Type II secretion system (T2SS), protein K / Type II secretion system (T2SS), protein K / Type II secretion system protein GspI, C-terminal / Type II secretion system protein GspI / Type II secretion system (T2SS), protein I / Type II secretion system protein GspJ ...General secretion pathway protein K / GspK, central domain superfamily / : / : / Type II secretion system (T2SS), protein K / Type II secretion system (T2SS), protein K / Type II secretion system protein GspI, C-terminal / Type II secretion system protein GspI / Type II secretion system (T2SS), protein I / Type II secretion system protein GspJ / Type II secretion system (T2SS), protein J / : / Prokaryotic N-terminal methylation site. / Prokaryotic N-terminal methylation motif / Prokaryotic N-terminal methylation site / Pilin-like
Similarity search - Domain/homology
Type II secretion system protein I / Type II secretion system protein J / Type II secretion system protein K
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsZhang, Y. / Wang, S. / Jia, Z.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)38855 Canada
CitationJournal: Int J Mol Sci / Year: 2020
Title: In Situ Proteolysis Condition-Induced Crystallization of the XcpVWX Complex in Different Lattices.
Authors: Zhang, Y. / Wang, S. / Jia, Z.
History
DepositionOct 30, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Type II secretion system protein I
B: Type II secretion system protein J
C: Type II secretion system protein K
D: Type II secretion system protein I
E: Type II secretion system protein J
F: Type II secretion system protein K
G: Type II secretion system protein I
H: Type II secretion system protein J
I: Type II secretion system protein K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)190,54618
Polymers190,1859
Non-polymers3619
Water362
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16860 Å2
ΔGint-93 kcal/mol
Surface area62490 Å2
Unit cell
Length a, b, c (Å)158.100, 158.100, 64.700
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number143
Space group name H-MP3
Space group name HallP3
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z

-
Components

#1: Protein Type II secretion system protein I / T2SS protein I / General secretion pathway protein I / PilD-dependent protein PddC


Mass: 10534.801 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: xcpV, pddC, PA3099 / Production host: Escherichia coli (E. coli) / References: UniProt: Q00516
#2: Protein Type II secretion system protein J / T2SS protein J / General secretion pathway protein J / PilD-dependent protein PddD


Mass: 22247.691 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: xcpW, pddD, PA3098 / Production host: Escherichia coli (E. coli) / References: UniProt: Q00517
#3: Protein Type II secretion system protein K / T2SS protein K / General secretion pathway protein K


Mass: 30612.576 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: xcpX, PA3097 / Production host: Escherichia coli (E. coli) / References: UniProt: Q00518
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 49.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 19 %-22 % PEG 2000 MME, 0.1 M Tris, pH 8.0-9.0, 0.2 M trimethylamine N-oxide (TMAO)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 X 1M / Detector: PIXEL / Date: Nov 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.83→19.91 Å / Num. obs: 42465 / % possible obs: 99.2 % / Redundancy: 10 % / Biso Wilson estimate: 79.02 Å2 / CC1/2: 0.998 / Net I/σ(I): 12.77
Reflection shellResolution: 2.83→3 Å / Num. unique obs: 6545 / CC1/2: 0.646

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
Blu-Icedata collection
XDSdata reduction
XDSdata scaling
PHENIXmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5VTM

5vtm


Resolution: 2.85→19.91 Å / SU ML: 0.4998 / Cross valid method: FREE R-VALUE / σ(F): 1.94 / Phase error: 31.2807
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2941 2108 5 %
Rwork0.2143 40044 -
obs0.2183 42152 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 73.29 Å2
Refinement stepCycle: LAST / Resolution: 2.85→19.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10549 0 9 2 10560
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00910731
X-RAY DIFFRACTIONf_angle_d1.102114598
X-RAY DIFFRACTIONf_chiral_restr0.0541656
X-RAY DIFFRACTIONf_plane_restr0.00611921
X-RAY DIFFRACTIONf_dihedral_angle_d18.47581530
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.85-2.920.37941410.28432687X-RAY DIFFRACTION100
2.92-2.990.39521410.27212668X-RAY DIFFRACTION100
2.99-3.070.34011390.2592653X-RAY DIFFRACTION100
3.07-3.160.36631430.25262701X-RAY DIFFRACTION100
3.16-3.260.32361400.25122670X-RAY DIFFRACTION100
3.26-3.380.35231390.24652645X-RAY DIFFRACTION100
3.38-3.510.33671400.21842648X-RAY DIFFRACTION100
3.51-3.670.28721400.21832663X-RAY DIFFRACTION100
3.67-3.860.30541410.21862683X-RAY DIFFRACTION100
3.86-4.10.31551410.21492673X-RAY DIFFRACTION100
4.1-4.420.28171390.19872654X-RAY DIFFRACTION100
4.42-4.850.26381420.1922689X-RAY DIFFRACTION100
4.85-5.540.26221400.20982656X-RAY DIFFRACTION100
5.54-6.930.28281400.22132674X-RAY DIFFRACTION100
6.94-19.910.26041420.18872680X-RAY DIFFRACTION99.96

+
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