[English] 日本語
Yorodumi
- PDB-5ay6: 32 kDa Fragment of the Flagellar hook protein FlgE from Caulobact... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ay6
Title32 kDa Fragment of the Flagellar hook protein FlgE from Caulobacter crescentus
ComponentsFlagellar hook protein FlgE
KeywordsMOTOR PROTEIN / Flagellum / Hook / Universal joint
Function / homology
Function and homology information


bacterial-type flagellum basal body / bacterial-type flagellum-dependent swarming motility
Similarity search - Function
: / Flagellar hook protein FlgE, second domain / 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 hook protein FlgE, second domain / 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 speciesCaulobacter crescentus CB15 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.839 Å
AuthorsYoon, Y.-H. / Matsunami, H. / Samatey, F.A.
CitationJournal: Sci Rep / Year: 2016
Title: Structural insights into bacterial flagellar hooks similarities and specificities
Authors: Yoon, Y.-H. / Barker, C.S. / Bulieris, P.V. / Matsunami, H. / Samatey, F.A.
History
DepositionAug 10, 2015Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 17, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2016Group: Database references
Revision 1.2Aug 30, 2017Group: Data collection / Derived calculations
Category: diffrn_detector / diffrn_source / pdbx_struct_oper_list
Item: _diffrn_detector.detector / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Oct 4, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.4Mar 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 hook protein FlgE
B: Flagellar hook protein FlgE


Theoretical massNumber of molelcules
Total (without water)63,1472
Polymers63,1472
Non-polymers00
Water20,0691114
1
A: Flagellar hook protein FlgE


Theoretical massNumber of molelcules
Total (without water)31,5741
Polymers31,5741
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Flagellar hook protein FlgE


Theoretical massNumber of molelcules
Total (without water)31,5741
Polymers31,5741
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.117, 61.580, 103.347
Angle α, β, γ (deg.)90.00, 91.92, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Flagellar hook protein FlgE


Mass: 31573.648 Da / Num. of mol.: 2 / Fragment: UNP residues 165-470
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caulobacter crescentus CB15 (bacteria) / Strain: CB15 / Gene: flgE, flaK, CC_0902 / Production host: Escherichia coli (E. coli) / References: UniProt: P35806
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1114 / 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: 2.78 Å3/Da / Density % sol: 55.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 0.1 M TAPS, 1 M Potassium citrate, 5% 1,5-pentanediol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9, 0.9791
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Oct 11, 2012
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.91
20.97911
ReflectionResolution: 1.839→19.785 Å / Num. obs: 53991 / % possible obs: 89.59 % / Redundancy: 3.7 % / Net I/σ(I): 4
Reflection shellResolution: 1.84→1.87 Å / % possible all: 85.2

-
Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.839→19.785 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 20.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2216 2753 5.1 %
Rwork0.1763 --
obs0.1785 53991 89.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.839→19.785 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4402 0 0 1114 5516
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044478
X-RAY DIFFRACTIONf_angle_d0.9316128
X-RAY DIFFRACTIONf_dihedral_angle_d11.411594
X-RAY DIFFRACTIONf_chiral_restr0.035732
X-RAY DIFFRACTIONf_plane_restr0.007808
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8392-1.87090.30431000.29451790X-RAY DIFFRACTION63
1.8709-1.90490.32311050.25931962X-RAY DIFFRACTION70
1.9049-1.94150.28961150.23912285X-RAY DIFFRACTION80
1.9415-1.98110.26221220.22512416X-RAY DIFFRACTION85
1.9811-2.02410.26231400.21162388X-RAY DIFFRACTION85
2.0241-2.07120.24691320.20542500X-RAY DIFFRACTION87
2.0712-2.12290.22241400.1912507X-RAY DIFFRACTION88
2.1229-2.18020.26391340.18282550X-RAY DIFFRACTION90
2.1802-2.24430.25991410.18692527X-RAY DIFFRACTION90
2.2443-2.31660.21871320.17922589X-RAY DIFFRACTION90
2.3166-2.39930.22481330.17352643X-RAY DIFFRACTION92
2.3993-2.49520.2151430.17922613X-RAY DIFFRACTION93
2.4952-2.60850.2311500.1752675X-RAY DIFFRACTION94
2.6085-2.74570.24181490.18082739X-RAY DIFFRACTION95
2.7457-2.91720.22981460.17272750X-RAY DIFFRACTION96
2.9172-3.14160.19751500.16462787X-RAY DIFFRACTION98
3.1416-3.45630.1911550.16342840X-RAY DIFFRACTION98
3.4563-3.95290.18531500.14742864X-RAY DIFFRACTION99
3.9529-4.96720.18891540.14062868X-RAY DIFFRACTION99
4.9672-19.78640.19281620.15832945X-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