[English] 日本語
Yorodumi
- PDB-6ndw: Crystal structure of the wild type D2 domain (A168-T344) of the f... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ndw
TitleCrystal structure of the wild type D2 domain (A168-T344) of the flagellar hook protein FlgE from Treponema denticola
ComponentsFlagellar hook protein FlgE
KeywordsMOTOR PROTEIN / hook / lysinoalanine / crosslinking / spirochetes / periodontal disease / FlgE
Function / homology
Function and homology information


bacterial-type flagellum basal body / bacterial-type flagellum-dependent swarming motility
Similarity search - Function
Flagellar hook protein FlgE superfamily / Flagellar hook protein FlgE / Flagellar basal body protein FlaE D2 domain / Flagellar hook-basal body protein, FlgE/F/G / Flagellar hook-basal body protein, FlgE/F/G-like / : / Flagellar hook protein FlgE/F/G D1 domain / Flagellar basal body rod protein, conserved site / Flagella basal body rod proteins signature. / Flagellar basal body rod protein, N-terminal ...Flagellar hook protein FlgE superfamily / Flagellar hook protein FlgE / Flagellar basal body protein FlaE D2 domain / Flagellar hook-basal body protein, FlgE/F/G / Flagellar hook-basal body protein, FlgE/F/G-like / : / Flagellar hook protein FlgE/F/G D1 domain / Flagellar basal body rod protein, conserved site / Flagella basal body rod proteins signature. / Flagellar basal body rod protein, N-terminal / Flagellar basal-body/hook protein, C-terminal domain / Flagella basal body rod protein / Flagellar basal body rod FlgEFG protein C-terminal
Similarity search - Domain/homology
Flagellar hook protein FlgE
Similarity search - Component
Biological speciesTreponema denticola (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.725 Å
AuthorsLynch, M.J. / Crane, B.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R35-122535 United States
CitationJournal: Nat.Chem.Biol. / Year: 2019
Title: Structure and chemistry of lysinoalanine crosslinking in the spirochaete flagella hook.
Authors: Lynch, M.J. / Miller, M. / James, M. / Zhang, S. / Zhang, K. / Li, C. / Charon, N.W. / Crane, B.R.
History
DepositionDec 14, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2019Group: Data collection / Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 9, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 11, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Flagellar hook protein FlgE


Theoretical massNumber of molelcules
Total (without water)19,1211
Polymers19,1211
Non-polymers00
Water4,486249
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)33.104, 61.290, 43.790
Angle α, β, γ (deg.)90.00, 104.45, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Flagellar hook protein FlgE


Mass: 19120.783 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Treponema denticola (bacteria) / Gene: flgE / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9RQB6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 249 / 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: 2.25 Å3/Da / Density % sol: 45.33 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 100 mM HEPES, 2.0M Ammonium sulfate

-
Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.977 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 27, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 1.725→50 Å / Num. obs: 17865 / % possible obs: 99.6 % / Redundancy: 6.6 % / Net I/σ(I): 24.5
Reflection shellResolution: 1.73→1.78 Å

-
Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WLG

1wlg


Resolution: 1.725→24.838 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 18.2
RfactorNum. reflection% reflectionSelection details
Rfree0.1868 1786 10 %random selection
Rwork0.1589 ---
obs0.1617 17858 99.55 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.725→24.838 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1338 0 0 249 1587
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061363
X-RAY DIFFRACTIONf_angle_d0.7751862
X-RAY DIFFRACTIONf_dihedral_angle_d12.668803
X-RAY DIFFRACTIONf_chiral_restr0.055215
X-RAY DIFFRACTIONf_plane_restr0.005250
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7247-1.77130.2331290.17581167X-RAY DIFFRACTION94
1.7713-1.82340.21721380.17211244X-RAY DIFFRACTION100
1.8234-1.88220.21971380.16931237X-RAY DIFFRACTION100
1.8822-1.94950.20261360.16161222X-RAY DIFFRACTION100
1.9495-2.02750.19281360.15231234X-RAY DIFFRACTION100
2.0275-2.11970.17681370.14971228X-RAY DIFFRACTION100
2.1197-2.23140.19011380.15011242X-RAY DIFFRACTION100
2.2314-2.37110.18091390.15921248X-RAY DIFFRACTION100
2.3711-2.5540.18051380.15611243X-RAY DIFFRACTION100
2.554-2.81070.20281370.17021242X-RAY DIFFRACTION100
2.8107-3.21670.17881390.15851241X-RAY DIFFRACTION100
3.2167-4.04990.17861380.14491253X-RAY DIFFRACTION100
4.0499-24.84060.1761430.1681271X-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