[English] 日本語
Yorodumi
- PDB-5npy: Crystal structure of Helicobacter pylori flagellar hook protein FlgE2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5npy
TitleCrystal structure of Helicobacter pylori flagellar hook protein FlgE2
ComponentsFlagellar basal body protein
KeywordsMOTOR PROTEIN / Helicobactyer pylori / flagellum / hook
Function / homology
Function and homology information


bacterial-type flagellum basal body / bacterial-type flagellum-dependent cell motility
Similarity search - Function
Flagellar basal body rod protein, conserved site / Flagellar hook-basal body protein, FlgE/F/G / Flagellar hook-basal body protein, FlgE/F/G-like / Flagella basal body rod proteins signature. / Flagellar basal-body/hook protein, C-terminal domain / Flagellar basal body rod FlgEFG protein C-terminal
Similarity search - Domain/homology
TRIS-HYDROXYMETHYL-METHYL-AMMONIUM / Flagellar basal body protein
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.292 Å
AuthorsLoconte, V. / Zanotti, G. / Kekez, I. / Matkovic-Calogovic, D.
CitationJournal: FEBS J. / Year: 2017
Title: Structural characterization of FlgE2 protein from Helicobacter pylori hook.
Authors: Loconte, V. / Kekez, I. / Matkovic-Calogovic, D. / Zanotti, G.
History
DepositionApr 19, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 15, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 27, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Flagellar basal body protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,0272
Polymers68,9051
Non-polymers1221
Water5,549308
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area300 Å2
ΔGint3 kcal/mol
Surface area22510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.209, 49.592, 238.261
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Flagellar basal body protein


Mass: 68904.969 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: G27 / Gene: flgE-2, HPG27_859 / Plasmid: pETit-hp0908 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B5Z7R4
#2: Chemical ChemComp-144 / TRIS-HYDROXYMETHYL-METHYL-AMMONIUM


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 308 / 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: 2.32 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M Potassium Thiocyanate, 0.1 M Bis-Tris Propane pH 8.5, 20% w/v PEG3350

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF ID23-210.8729
SYNCHROTRONESRF ID23-120.98127
Detector
TypeIDDetectorDate
DECTRIS PILATUS 2M1PIXELMay 12, 2016
DECTRIS PILATUS3 S 6M2PIXELMar 21, 2017
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.87291
20.981271
ReflectionResolution: 2.29→48.551 Å / Num. obs: 23979 / % possible obs: 98.5 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.148 / Rpim(I) all: 0.076 / Net I/σ(I): 9.7
Reflection shellResolution: 2.29→2.4 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.671 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 3106 / Rpim(I) all: 0.362 / % possible all: 90.8

-
Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
iMOSFLMdata reduction
Aimlessdata scaling
autoSHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.292→48.551 Å / SU ML: 0.35 / Data cutoff high absF: 0 / Data cutoff low absF: 0 / Cross valid method: FREE R-VALUE / σ(F): 1.25 / Phase error: 28.21
RfactorNum. reflection% reflection
Rfree0.2661 2133 4.97 %
Rwork0.1881 --
obs0.192 23686 96.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.292→48.551 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3715 0 8 308 4031
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083792
X-RAY DIFFRACTIONf_angle_d0.9955112
X-RAY DIFFRACTIONf_dihedral_angle_d15.2792311
X-RAY DIFFRACTIONf_chiral_restr0.058553
X-RAY DIFFRACTIONf_plane_restr0.007669
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2922-2.34550.28871060.24042091X-RAY DIFFRACTION74
2.3455-2.40420.3331480.24072786X-RAY DIFFRACTION99
2.4042-2.46920.37551490.25862765X-RAY DIFFRACTION99
2.4692-2.54180.32851460.25152794X-RAY DIFFRACTION99
2.5418-2.62390.36731460.25562778X-RAY DIFFRACTION99
2.6239-2.71770.31681360.25182756X-RAY DIFFRACTION98
2.7177-2.82650.32821380.24742712X-RAY DIFFRACTION98
2.8265-2.95510.29991480.2342777X-RAY DIFFRACTION99
2.9551-3.11080.32081450.21072826X-RAY DIFFRACTION99
3.1108-3.30570.24131450.18622795X-RAY DIFFRACTION99
3.3057-3.56090.31211410.1792755X-RAY DIFFRACTION99
3.5609-3.91910.25041440.16932719X-RAY DIFFRACTION97
3.9191-4.48580.19881450.12982707X-RAY DIFFRACTION97
4.4858-5.65030.20541450.1322769X-RAY DIFFRACTION99
5.6503-48.56230.20881510.17132779X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 36.8348 Å / Origin y: -0.1189 Å / Origin z: 227.6481 Å
111213212223313233
T0.1647 Å20.003 Å20.022 Å2-0.1652 Å2-0.0042 Å2--0.1703 Å2
L0.1009 °2-0.0833 °20.0204 °2-0.1709 °2-0.1689 °2--0.5528 °2
S0.0461 Å °0.0088 Å °-0.0151 Å °0.0219 Å °0.0423 Å °-0.0266 Å °-0.0914 Å °-0.0125 Å °0.0122 Å °
Refinement TLS groupSelection details: all

+
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