[English] 日本語
Yorodumi
- PDB-6bbk: N-terminally truncated group I PilA from Pseudomonas aeruginosa s... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6bbk
TitleN-terminally truncated group I PilA from Pseudomonas aeruginosa strain 1244
ComponentsFimbrial protein
KeywordsMEMBRANE PROTEIN / Pseudomonas aeruginosa / type IV pili / major pilin / pilin / pilus / twitching motility / adhesion / biofilm / virulence / filament / subunit
Function / homology
Function and homology information


protein secretion by the type II secretion system / type II protein secretion system complex / pilus / cell adhesion / membrane
Similarity search - Function
Bacterial general secretion pathway protein G-type pilin / Fimbrial protein pilin / Pilin (bacterial filament) / : / Prokaryotic N-terminal methylation site. / Prokaryotic N-terminal methylation motif / Prokaryotic N-terminal methylation site / Pilin-like
Similarity search - Domain/homology
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.73 Å
AuthorsShen, Y. / Guarne, A. / Nguyen, Y. / Burrows, L.L.
CitationJournal: To Be Published
Title: N-terminally truncated group I PilA from Pseudomonas aeruginosa strain 1244
Authors: Shen, Y. / Nguyen, Y. / Guarne, A. / Burrows, L.L.
History
DepositionOct 18, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Fimbrial protein


Theoretical massNumber of molelcules
Total (without water)13,2031
Polymers13,2031
Non-polymers00
Water2,144119
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology, Truncated type IV pilins are monomeric in the buffer conditions used.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)30.494, 42.394, 82.442
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Fimbrial protein / Pilin


Mass: 13202.734 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: pilA, fimA / Production host: Escherichia coli (E. coli) / Strain (production host): Origami2 / Variant (production host): non-reducing cytoplasm / References: UniProt: P18774
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / 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: 2.04 Å3/Da / Density % sol: 39.84 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES:NaOH, 20% (w/v) PEG 4000, 10% (v/v) 2-Propanol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→35 Å / Num. obs: 12215 / % possible obs: 98.8 % / Redundancy: 35.6 % / Biso Wilson estimate: 21.21 Å2 / Rmerge(I) obs: 0.051 / Χ2: 0.982 / Net I/σ(I): 19 / Num. measured all: 434970
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.7-1.73110.2184530.669178.2
1.73-1.76170.2156040.739197.6
1.76-1.7925.30.1996110.774199.3
1.79-1.8332.30.1865830.844199.5
1.83-1.8735.90.1626090.8711100
1.87-1.91380.1526200.938199.8
1.91-1.9638.50.1265831.0841100
1.96-2.0239.60.1116310.854199.8
2.02-2.0738.90.1035901.0591100
2.07-2.1439.40.0946101.2071100
2.14-2.2239.70.0836110.7491100
2.22-2.3138.90.0816101.1191100
2.31-2.4139.80.0726170.8991100
2.41-2.5439.90.0666160.8691100
2.54-2.739.70.0616160.8651100
2.7-2.9139.60.0536321.131100
2.91-3.239.40.0476241.0451100
3.2-3.6639.10.0426261.0431100
3.66-4.6138.20.0366600.9221100
4.61-3534.90.0317091.4561100

-
Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-3000data scaling
PDB_EXTRACT3.22data extraction
HKL-3000data reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.73→29.554 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2259 557 4.76 %
Rwork0.1861 11138 -
obs0.1882 11695 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 63.73 Å2 / Biso mean: 22.5606 Å2 / Biso min: 11.54 Å2
Refinement stepCycle: final / Resolution: 1.73→29.554 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms913 0 0 119 1032
Biso mean---28.85 -
Num. residues----124
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005975
X-RAY DIFFRACTIONf_angle_d0.7361339
X-RAY DIFFRACTIONf_chiral_restr0.054163
X-RAY DIFFRACTIONf_plane_restr0.005173
X-RAY DIFFRACTIONf_dihedral_angle_d2.308811
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.73-1.90410.29481240.20912730285499
1.9041-2.17950.24441450.189127442889100
2.1795-2.74570.26391320.201227682900100
2.7457-29.55790.19791560.174328963052100

+
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