[English] 日本語
Yorodumi
- PDB-7dm9: Crystal structure of FliM middle domain (51-229) from Vibro algin... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7dm9
TitleCrystal structure of FliM middle domain (51-229) from Vibro alginolyticus
ComponentsFlagellar motor switch protein FliM
KeywordsMOTOR PROTEIN / Flagellar motor protein
Function / homology
Function and homology information


bacterial-type flagellum basal body / cytoskeletal motor activity / bacterial-type flagellum-dependent cell motility / chemotaxis / plasma membrane
Similarity search - Function
CheC-like / Chemotaxis protein chec / Flagellar motor switch protein FliM / Flagellar motor switch protein FliM / 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Flagellar motor switch protein FliM
Similarity search - Component
Biological speciesVibrio alginolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 Å
AuthorsTakekawa, N. / Homma, M. / Imada, K.
Funding support Japan, 5items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP16J01859 Japan
Japan Society for the Promotion of Science (JSPS)JP17J11237 Japan
Japan Society for the Promotion of Science (JSPS)JP20J00329 Japan
Japan Society for the Promotion of Science (JSPS)JP18K19293 Japan
Japan Society for the Promotion of Science (JSPS)JP20H03220 Japan
CitationJournal: J.Biochem. / Year: 2021
Title: A slight bending of an alpha-helix in FliM creates a counterclockwise-locked structure of the flagellar motor in Vibrio.
Authors: Takekawa, N. / Nishikino, T. / Yamashita, T. / Hori, K. / Onoue, Y. / Ihara, K. / Kojima, S. / Homma, M. / Imada, K.
History
DepositionDec 2, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 7, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 22, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Flagellar motor switch protein FliM


Theoretical massNumber of molelcules
Total (without water)22,2741
Polymers22,2741
Non-polymers00
Water1,76598
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8260 Å2
Unit cell
Length a, b, c (Å)29.580, 62.500, 73.890
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 Flagellar motor switch protein FliM


Mass: 22273.840 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The N-terminal GSHM is a remnant of the His-tag / Source: (gene. exp.) Vibrio alginolyticus (bacteria)
Gene: Vag1382_20640, VagVIO5_20640, VagYM19_20670, VagYM4_20660
Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A6F8W0A1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 1.53 Å3/Da / Density % sol: 19.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9.5 / Details: 40 % (w/v) PEG-600, 0.1 M CHES-NaOH

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 29, 2019
RadiationMonochromator: Double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.71→73.89 Å / Num. obs: 15496 / % possible obs: 100 % / Redundancy: 5.9 % / Biso Wilson estimate: 19.4 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.044 / Rrim(I) all: 0.079 / Net I/σ(I): 14.3
Reflection shellResolution: 1.71→1.74 Å / Redundancy: 6 % / Rmerge(I) obs: 0.264 / Mean I/σ(I) obs: 5.7 / Num. unique obs: 824 / CC1/2: 0.959 / Rpim(I) all: 0.176 / Rrim(I) all: 0.319 / % possible all: 100

-
Processing

Software
NameVersionClassification
BSSdata collection
iMOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing
Cootmodel building
PHENIX1.18.2_3874refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5X0Z

5x0z


Resolution: 1.71→47.72 Å / SU ML: 0.1761 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.7224
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2073 762 4.94 %
Rwork0.1731 14676 -
obs0.1748 15438 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.33 Å2
Refinement stepCycle: LAST / Resolution: 1.71→47.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1364 0 0 98 1462
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00881467
X-RAY DIFFRACTIONf_angle_d1.17691994
X-RAY DIFFRACTIONf_chiral_restr0.0698223
X-RAY DIFFRACTIONf_plane_restr0.0067260
X-RAY DIFFRACTIONf_dihedral_angle_d24.6357559
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.71-1.840.25911520.20042876X-RAY DIFFRACTION99.84
1.84-2.030.24021600.17182859X-RAY DIFFRACTION99.83
2.03-2.320.21731240.16962940X-RAY DIFFRACTION99.97
2.32-2.920.22851660.17922917X-RAY DIFFRACTION99.87
2.92-47.720.17751600.16763084X-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