[English] 日本語
Yorodumi
- PDB-4fhr: Crystal structure of the complex between the flagellar motor prot... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4fhr
TitleCrystal structure of the complex between the flagellar motor proteins FliG and FliM.
Components
  • Flagellar motor switch protein FliG
  • Flagellar motor switch protein FliM
KeywordsMOTOR PROTEIN / flagellar motor
Function / homology
Function and homology information


bacterial-type flagellum basal body / bacterial-type flagellum-dependent swarming motility / positive chemotaxis / cytoskeletal motor activity / bacterial-type flagellum-dependent cell motility / chemotaxis / protein heterodimerization activity / protein homodimerization activity / plasma membrane
Similarity search - Function
Flagellar motor switch protein FliG, alpha-alpha superhelical domain / CheC-like / Chemotaxis protein chec / Flagellar motor switch protein FliM / Flagellar motor switch protein FliM / 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 ...Flagellar motor switch protein FliG, alpha-alpha superhelical domain / CheC-like / Chemotaxis protein chec / Flagellar motor switch protein FliM / Flagellar motor switch protein FliM / 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 / CheC-like superfamily / Flagellar motor switch protein FliN-like, C-terminal domain / SpoA-like superfamily / Type III flagellar switch regulator (C-ring) FliN C-term / Annexin V; domain 1 / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Flagellar motor switch protein FliG / Flagellar motor switch protein FliM
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.931 Å
AuthorsPaz, A. / Vartanian, A.S. / Fortgang, E.A. / Abramson, J. / Dahlquist, F.W.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Structure of flagellar motor proteins in complex allows for insights into motor structure and switching.
Authors: Vartanian, A.S. / Paz, A. / Fortgang, E.A. / Abramson, J. / Dahlquist, F.W.
History
DepositionJun 6, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 22, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 7, 2012Group: Database references
Revision 1.2Sep 13, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Flagellar motor switch protein FliM
B: Flagellar motor switch protein FliG


Theoretical massNumber of molelcules
Total (without water)46,0952
Polymers46,0952
Non-polymers00
Water1,946108
1
A: Flagellar motor switch protein FliM


Theoretical massNumber of molelcules
Total (without water)21,4911
Polymers21,4911
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Flagellar motor switch protein FliG


Theoretical massNumber of molelcules
Total (without water)24,6051
Polymers24,6051
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)125.960, 45.720, 98.840
Angle α, β, γ (deg.)90.00, 100.85, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Flagellar motor switch protein FliM


Mass: 21490.619 Da / Num. of mol.: 1 / Fragment: Middle domain, UNP residues 46-230
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: FliM / Plasmid: pJY5 / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21 Rosetta / References: UniProt: Q9WZE6
#2: Protein Flagellar motor switch protein FliG


Mass: 24604.529 Da / Num. of mol.: 1
Fragment: Middle and C-terminal domains. UNP residues 115-327
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: fliG / Plasmid: pJY5 / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21 Rosetta / References: UniProt: Q9WY63
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / 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: 3.03 Å3/Da / Density % sol: 59.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 50 mM calcium acetate, 0.1 M sodium cacodylate pH 6.0, and 25% v/v MPD, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 31, 2010
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.93→50 Å / Num. all: 41987 / Num. obs: 38741 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellResolution: 1.93→2 Å / % possible all: 99.8

-
Processing

Software
NameVersionClassification
BOSdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HP7

2hp7


Resolution: 1.931→48.537 Å / SU ML: 0.2 / σ(F): 0.1 / Phase error: 24.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2431 1968 5.08 %
Rwork0.2084 --
obs0.2102 38741 92.29 %
all-38740 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.4488 Å20 Å2-0.3035 Å2
2--3.2599 Å2-0 Å2
3----2.8111 Å2
Refinement stepCycle: LAST / Resolution: 1.931→48.537 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3138 0 0 108 3246
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083207
X-RAY DIFFRACTIONf_angle_d1.0594340
X-RAY DIFFRACTIONf_dihedral_angle_d15.6241239
X-RAY DIFFRACTIONf_chiral_restr0.07506
X-RAY DIFFRACTIONf_plane_restr0.006560
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9311-1.97940.3104890.27241583X-RAY DIFFRACTION55
1.9794-2.03290.33641270.26542389X-RAY DIFFRACTION86
2.0329-2.09270.29691400.24582601X-RAY DIFFRACTION92
2.0927-2.16030.29931390.23812601X-RAY DIFFRACTION92
2.1603-2.23750.27881390.23472603X-RAY DIFFRACTION92
2.2375-2.32710.24741410.21742649X-RAY DIFFRACTION94
2.3271-2.4330.26161440.21222692X-RAY DIFFRACTION95
2.433-2.56120.23731470.2142750X-RAY DIFFRACTION97
2.5612-2.72170.26751470.22712756X-RAY DIFFRACTION97
2.7217-2.93180.26631480.22182789X-RAY DIFFRACTION98
2.9318-3.22680.23181520.2212836X-RAY DIFFRACTION99
3.2268-3.69360.25851520.20412844X-RAY DIFFRACTION100
3.6936-4.6530.19821530.17222859X-RAY DIFFRACTION99
4.653-48.55190.20381500.18552821X-RAY DIFFRACTION95

+
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