[English] 日本語
Yorodumi
- PDB-4noa: Truncated minor pilin PilE from Pseudomonas aeruginosa -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4noa
TitleTruncated minor pilin PilE from Pseudomonas aeruginosa
ComponentsType 4 fimbrial biogenesis protein PilE
KeywordsUNKNOWN FUNCTION
Function / homology
Function and homology information


type IV pilus assembly / type IV pilus-dependent motility / pilus assembly / plasma membrane
Similarity search - Function
Type IV pilus non-core minor pilin PilE-like / Type IV minor pilin ComP, DNA uptake sequence receptor / : / Prokaryotic N-terminal methylation site. / Prokaryotic N-terminal methylation motif / Prokaryotic N-terminal methylation site / Pilin-like
Similarity search - Domain/homology
Type IV pilus non-core minor pilin PilE
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.25 Å
AuthorsNguyen, Y. / Sugiman-Marangos, S.N. / Bell, S. / Junop, M.S. / Burrows, L.L.
CitationJournal: To be Published
Title: Crystal structure of truncated minor pilin PilE from Pseudomonas aeruginosa
Authors: Nguyen, Y. / Sugiman-Marangos, S.N. / Bell, S. / Harvey, H. / Junop, M.S. / Burrows, L.L.
History
DepositionNov 19, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 19, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Type 4 fimbrial biogenesis protein PilE


Theoretical massNumber of molelcules
Total (without water)12,0931
Polymers12,0931
Non-polymers00
Water4,396244
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)76.159, 35.560, 43.536
Angle α, β, γ (deg.)90.00, 97.33, 90.00
Int Tables number5
Space group name H-MC121
DetailsAUTHORS STATE THAT THE BIOLOGICAL ASSEMBLY IN UNKNOWN.

-
Components

#1: Protein Type 4 fimbrial biogenesis protein PilE


Mass: 12093.130 Da / Num. of mol.: 1 / Fragment: UNP residues 36-141
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: PA4556, pilE / Plasmid: pET151-D-topo / Production host: Escherichia coli (E. coli) / Strain (production host): Origami B(DE3) / References: UniProt: G3XD43
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 244 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.2 M Ammonium tartrate dibasic, 20% (w/v) PEG 3350, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.979 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 25, 2012 / Details: Mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.25→50 Å / Num. all: 30749 / Num. obs: 30749 / % possible obs: 95.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Biso Wilson estimate: 8.28 Å2 / Rmerge(I) obs: 0.084 / Rsym value: 0.084 / Net I/σ(I): 20.7
Reflection shellResolution: 1.25→1.27 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 7.6 / Num. unique all: 1462 / Rsym value: 0.21 / % possible all: 89.6

-
Processing

Software
NameVersionClassification
CBASSdata collection
PHENIX(phenix.autosol)model building
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.25→43.181 Å / SU ML: 0.12 / σ(F): 0 / Phase error: 14.68 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.1753 1996 6.51 %Random
Rwork0.159 ---
obs0.1601 30645 94.82 %-
all-30645 --
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.969 Å2 / ksol: 0.442 e/Å3
Displacement parametersBiso mean: 11.51 Å2
Baniso -1Baniso -2Baniso -3
1-1.1712 Å20 Å21.8603 Å2
2--1.2334 Å2-0 Å2
3----2.4046 Å2
Refinement stepCycle: LAST / Resolution: 1.25→43.181 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms810 0 0 244 1054
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005850
X-RAY DIFFRACTIONf_angle_d0.9651166
X-RAY DIFFRACTIONf_dihedral_angle_d10.136320
X-RAY DIFFRACTIONf_chiral_restr0.063136
X-RAY DIFFRACTIONf_plane_restr0.004156
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.25-1.27970.19611310.18651873X-RAY DIFFRACTION87
1.2797-1.31430.18021400.1781993X-RAY DIFFRACTION92
1.3143-1.3530.1811370.16371952X-RAY DIFFRACTION92
1.353-1.39670.18391400.16432002X-RAY DIFFRACTION94
1.3967-1.44660.16081400.14932015X-RAY DIFFRACTION94
1.4466-1.50450.18021390.14452012X-RAY DIFFRACTION94
1.5045-1.5730.15941410.14212015X-RAY DIFFRACTION95
1.573-1.65590.15341430.13582054X-RAY DIFFRACTION95
1.6559-1.75970.17111450.1452080X-RAY DIFFRACTION96
1.7597-1.89560.19461450.15772089X-RAY DIFFRACTION97
1.8956-2.08630.18541450.16092082X-RAY DIFFRACTION97
2.0863-2.38820.17651470.15562106X-RAY DIFFRACTION98
2.3882-3.00880.17421510.1682165X-RAY DIFFRACTION98
3.0088-43.20650.17031520.16472211X-RAY DIFFRACTION99

+
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