[English] 日本語
Yorodumi
- PDB-5wuj: Crystal structure of FliF-FliG complex from H. pylori -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5wuj
TitleCrystal structure of FliF-FliG complex from H. pylori
Components
  • Flagellar M-ring protein
  • Flagellar motor switch protein FliGFlagellar motor switch protein
KeywordsMOTOR PROTEIN / flagellar motor / MS-ring / C-ring
Function / homology
Function and homology information


bacterial-type flagellum basal body, MS ring / bacterial-type flagellum basal body / bacterial-type flagellum / bacterial-type flagellum-dependent swarming motility / cytoskeletal motor activity / bacterial-type flagellum-dependent cell motility / chemotaxis / membrane => GO:0016020 / plasma membrane
Similarity search - Function
Flagellar motor switch protein FliG / Flagellar motor switch protein FliG, alpha-helical / Flagellar motor switch protein FliG, C-terminal / Flagellar motor switch protein FliG, N-terminal domain / Flagellar motor switch protein FliG, middle domain / FliG C-terminal domain / FliG middle domain / FliG N-terminal domain / Flagellar M-ring protein FliF / Flagellar M-ring C-terminal ...Flagellar motor switch protein FliG / Flagellar motor switch protein FliG, alpha-helical / Flagellar motor switch protein FliG, C-terminal / Flagellar motor switch protein FliG, N-terminal domain / Flagellar motor switch protein FliG, middle domain / FliG C-terminal domain / FliG middle domain / FliG N-terminal domain / Flagellar M-ring protein FliF / Flagellar M-ring C-terminal / Flagellar M-ring protein C-terminal / Lipoprotein YscJ/Flagellar M-ring protein / Secretory protein of YscJ/FliF family / Flagellar M-ring , N-terminal
Similarity search - Domain/homology
Flagellar M-ring protein / Flagellar motor switch protein FliG
Similarity search - Component
Biological speciesHelicobacter pylori 26695 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsAu, S.W. / Xue, C. / Lam, K.H. / Lee, S.H.
Funding support Hong Kong, 1items
OrganizationGrant numberCountry
GRFGRF 460112 Hong Kong
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Crystal structure of the FliF-FliG complex from Helicobacter pylori yields insight into the assembly of the motor MS-C ring in the bacterial flagellum
Authors: Xue, C. / Lam, K.H. / Zhang, H. / Sun, K. / Lee, S.H. / Chen, X. / Au, S.W.N.
History
DepositionDec 19, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 3, 2018Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed
Revision 1.2Apr 4, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Flagellar M-ring protein
B: Flagellar motor switch protein FliG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3313
Polymers16,2392
Non-polymers921
Water81145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2950 Å2
ΔGint-23 kcal/mol
Surface area8650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.098, 61.098, 86.930
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

-
Components

#1: Protein/peptide Flagellar M-ring protein


Mass: 4502.252 Da / Num. of mol.: 1 / Fragment: C-terminal domain, residues 523-559
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori 26695 (bacteria) / Strain: 26695 / Gene: HP_0351
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): 'BL21-Gold(DE3)pLysS AG' / References: UniProt: O25118
#2: Protein Flagellar motor switch protein FliG / Flagellar motor switch protein / Flagellar motor switch protein G


Mass: 11736.369 Da / Num. of mol.: 1 / Fragment: N-terminal domain, residues 7-111
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori 26695 (bacteria) / Strain: 26695 / Gene: fliG
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): 'BL21-Gold(DE3)pLysS AG' / References: UniProt: O25119
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 45 / 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: 2.88 Å3/Da / Density % sol: 57.36 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.1 M Sodium citrate tribasic dihydrate, 20%(v/v) 2-Propanol, 20%(w/v) Polyethylene glycol 4000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 6, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.3→45.2 Å / Num. obs: 8475 / % possible obs: 96.6 % / Redundancy: 20.1 % / CC1/2: 0.994 / Rmerge(I) obs: 0.121 / Net I/σ(I): 17
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
2.3-2.3920.90.3360.992199.9
8.6-45.2110.1010.973195.8

-
Processing

Software
NameVersionClassification
MOSFLMdata collection
SCALA0.1.27data scaling
PHENIX(dev_2621: ???)refinement
PDB_EXTRACT3.22data extraction
MOSFLMdata reduction
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→45.198 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 23.34
RfactorNum. reflection% reflection
Rfree0.2237 417 4.94 %
Rwork0.1884 --
obs0.1902 8443 96.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 111.18 Å2 / Biso mean: 39.2752 Å2 / Biso min: 15.28 Å2
Refinement stepCycle: final / Resolution: 2.3→45.198 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1137 0 6 45 1188
Biso mean--64.15 37.3 -
Num. residues----142
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071158
X-RAY DIFFRACTIONf_angle_d0.811550
X-RAY DIFFRACTIONf_chiral_restr0.048184
X-RAY DIFFRACTIONf_plane_restr0.003196
X-RAY DIFFRACTIONf_dihedral_angle_d2.963724
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2996-2.63230.25951390.187427272866100
2.6323-3.31630.25321420.20752611275396
3.3163-45.20690.19831360.17952688282494
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)
16.0579-1.5803-3.73095.43912.25523.1843-0.0395-0.32810.17490.46470.3526-0.09730.55480.1789-0.36460.24660.0376-0.03490.22950.02380.21730.0742-12.42837.4797
22.1239-2.45110.76517.1835-0.50117.97670.1792-0.2566-0.204-0.3617-0.20370.698-0.0799-0.5064-0.06050.2138-0.0316-0.04830.2782-0.09490.272424.0439-15.134-11.9916
34.717-2.4627-3.39195.52022.23792.53250.0928-0.73810.49150.4957-0.10980.7955-0.8308-3.1088-0.09310.48070.2090.03090.8854-0.09210.481411.0675-3.67272.9406
45.03870.2229-3.54946.00510.73572.68050.2353-0.0262-0.2647-0.391-0.133-0.251-0.40060.0571-0.13430.25060.0232-0.01810.20280.01480.192328.7198-6.7173-7.1669
55.3121-1.5145-4.47437.11693.93764.75890.11580.11690.131-0.1621-0.57641.0637-0.6405-0.44660.34810.3072-0.0069-0.04270.1743-0.0020.385823.43060.0454-9.1127
65.9674-3.3389-3.0572.75493.58397.2995-0.11040.0529-0.26590.3901-0.11390.61490.1585-0.2950.17810.1742-0.0245-0.00420.18150.03630.22521.5814-13.17632.7498
74.22511.8264-5.15272.4814-1.7567.5317-0.29070.1428-0.0828-0.1699-0.00140.23990.4901-0.00830.37250.3087-0.0341-0.04220.2154-0.01580.311321.671-22.03117.2171
84.5929-1.73113.34443.9745-3.39883.83670.5337-1.63450.49081.331-0.5797-0.35350.4614-0.47460.19220.6881-0.1359-0.09770.5788-0.040.423718.5213-24.463820.495
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 523 through 543 )A523 - 543
2X-RAY DIFFRACTION2chain 'A' and (resid 544 through 559 )A544 - 559
3X-RAY DIFFRACTION3chain 'B' and (resid 7 through 17 )B7 - 17
4X-RAY DIFFRACTION4chain 'B' and (resid 18 through 42 )B18 - 42
5X-RAY DIFFRACTION5chain 'B' and (resid 43 through 60 )B43 - 60
6X-RAY DIFFRACTION6chain 'B' and (resid 61 through 77 )B61 - 77
7X-RAY DIFFRACTION7chain 'B' and (resid 78 through 97 )B78 - 97
8X-RAY DIFFRACTION8chain 'B' and (resid 98 through 111 )B98 - 111

+
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