[English] 日本語
Yorodumi
- PDB-9jrv: Pilin PilA from Burkholderia cenocepacia -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9jrv
TitlePilin PilA from Burkholderia cenocepacia
ComponentsType IV pilin protein
KeywordsCELL ADHESION / Pilin / Burkholderia cenocepacia / adhesion protein
Function / homology
Function and homology information


pilus / cell adhesion / membrane
Similarity search - Function
Fimbrial protein pilin / Pilin (bacterial filament) / Prokaryotic N-terminal methylation motif / Prokaryotic N-terminal methylation site / Pilin-like
Similarity search - Domain/homology
ACETATE ION / Type IV pilin protein
Similarity search - Component
Biological speciesBurkholderia cenocepacia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsLotangchanintra, T. / Wangkanont, K.
Funding support Thailand, 1items
OrganizationGrant numberCountry
Thailand Science Research and Innovation Fund Chulalongkorn University Thailand
CitationJournal: To Be Published
Title: Pilin PilA from Burkholderia cenocepacia
Authors: Lotangchanintra, T. / Wangkanont, K.
History
DepositionSep 29, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 1, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Type IV pilin protein
B: Type IV pilin protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3175
Polymers29,1062
Non-polymers2103
Water7,656425
1
A: Type IV pilin protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6713
Polymers14,5531
Non-polymers1182
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-2 kcal/mol
Surface area7500 Å2
MethodPISA
2
B: Type IV pilin protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6452
Polymers14,5531
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.190, 62.160, 138.219
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

#1: Protein Type IV pilin protein


Mass: 14553.227 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia cenocepacia (bacteria) / Gene: pilA / Plasmid: pET-32b / Production host: Escherichia coli (E. coli) / References: UniProt: B4EBY9
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 425 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.56 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100 mM sodium cacodylate, 200 mM sodium acetate, 30% PEG 8,000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Apr 8, 2023
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.5→28.43 Å / Num. obs: 44186 / % possible obs: 100 % / Redundancy: 14.1 % / Biso Wilson estimate: 16.39 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.027 / Rrim(I) all: 0.103 / Χ2: 0.98 / Net I/σ(I): 15.1
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 10.1 % / Rmerge(I) obs: 1.185 / Mean I/σ(I) obs: 2 / Num. unique obs: 2118 / CC1/2: 0.749 / Rpim(I) all: 0.388 / Rrim(I) all: 1.248 / Χ2: 0.89 / % possible all: 100

-
Processing

Software
NameVersionClassification
MOSFLM7.4.0data reduction
Aimless0.7.9data scaling
PHASER2.8.3phasing
PHENIX1.20.1_4487model building
PHENIX1.20.1_4487refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→28.43 Å / SU ML: 0.1677 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.5152
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1956 2189 4.96 %
Rwork0.1484 41920 -
obs0.1508 44109 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.41 Å2
Refinement stepCycle: LAST / Resolution: 1.5→28.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2042 0 14 425 2481
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00572170
X-RAY DIFFRACTIONf_angle_d0.84082985
X-RAY DIFFRACTIONf_chiral_restr0.0536355
X-RAY DIFFRACTIONf_plane_restr0.0093403
X-RAY DIFFRACTIONf_dihedral_angle_d11.3021768
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.530.26341230.22362564X-RAY DIFFRACTION100
1.53-1.570.2951380.20092581X-RAY DIFFRACTION99.93
1.57-1.610.27671480.17462551X-RAY DIFFRACTION99.96
1.61-1.650.23911150.1612628X-RAY DIFFRACTION100
1.65-1.70.25361310.14822554X-RAY DIFFRACTION100
1.7-1.750.20321300.15232595X-RAY DIFFRACTION99.96
1.75-1.820.22441300.14932606X-RAY DIFFRACTION100
1.82-1.890.1871520.13832561X-RAY DIFFRACTION100
1.89-1.980.20691470.13152596X-RAY DIFFRACTION100
1.98-2.080.19491340.13542639X-RAY DIFFRACTION100
2.08-2.210.20531470.13922595X-RAY DIFFRACTION100
2.21-2.380.18241320.14142628X-RAY DIFFRACTION100
2.38-2.620.21841310.15262648X-RAY DIFFRACTION100
2.62-30.2231360.15482628X-RAY DIFFRACTION100
3-3.780.1591430.14162704X-RAY DIFFRACTION100
3.78-28.430.1671520.14752842X-RAY DIFFRACTION100

+
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