[English] 日本語
Yorodumi
- PDB-4gc8: Crystal structure of FliM middle domain from H. pylori -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4gc8
TitleCrystal structure of FliM middle domain from H. pylori
ComponentsFlagellar motor switch protein
KeywordsMOTOR PROTEIN / Flagellar motor switch / chemotaxis / flagellation / FliN / FliG / CheY
Function / homology
Function and homology information


bacterial-type flagellum basal body / bacterial-type flagellum-dependent swarming motility / positive chemotaxis / cytoskeletal motor activity / plasma membrane
Similarity search - Function
CheC-like / Chemotaxis protein chec / Flagellar motor switch protein FliM / Flagellar motor switch protein FliM / Flagellar motor switch protein FliN-like, C-terminal domain / SpoA-like superfamily / Type III flagellar switch regulator (C-ring) FliN C-term / CheC-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Flagellar motor switch protein FliM
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsLam, K.H. / Au, S.W.N.
CitationJournal: Mol.Microbiol. / Year: 2013
Title: Structural basis of FliG-FliM interaction in Helicobacter pylori
Authors: Lam, K.H. / Lam, W.W.L. / Wong, J.Y. / Chan, L.C. / Kotaka, M. / Ling, T.K.W. / Jin, D.Y. / Ottemann, K.M. / Au, S.W.N.
History
DepositionJul 30, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 8, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2013Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
B: Flagellar motor switch protein
C: Flagellar motor switch protein


Theoretical massNumber of molelcules
Total (without water)71,3303
Polymers71,3303
Non-polymers00
Water3,009167
1
A: Flagellar motor switch protein


Theoretical massNumber of molelcules
Total (without water)23,7771
Polymers23,7771
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Flagellar motor switch protein


Theoretical massNumber of molelcules
Total (without water)23,7771
Polymers23,7771
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Flagellar motor switch protein


Theoretical massNumber of molelcules
Total (without water)23,7771
Polymers23,7771
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)91.267, 91.267, 57.086
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

-
Components

#1: Protein Flagellar motor switch protein / / FliM


Mass: 23776.727 Da / Num. of mol.: 3 / Fragment: residues 31-237
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: 26695 / Gene: FliM / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: O25675
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 167 / 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: 1.92 Å3/Da / Density % sol: 36.08 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES, 25% PEG2250, 20mM Sodium Bromide, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 20, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 26406 / Biso Wilson estimate: 30.84 Å2

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8_1069)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→26.846 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8236 / SU ML: 0.3 / σ(F): 2.04 / Phase error: 25.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2373 1335 5.06 %
Rwork0.1755 --
obs0.1787 26406 97.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 127.08 Å2 / Biso mean: 36.1242 Å2 / Biso min: 11.77 Å2
Refinement stepCycle: LAST / Resolution: 2.2→26.846 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4140 0 0 167 4307
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084202
X-RAY DIFFRACTIONf_angle_d1.1175670
X-RAY DIFFRACTIONf_chiral_restr0.072679
X-RAY DIFFRACTIONf_plane_restr0.006714
X-RAY DIFFRACTIONf_dihedral_angle_d15.0791601
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2-2.27860.32311280.22962493262197
2.2786-2.36980.32331130.21422506261998
2.3698-2.47760.26191150.20222543265898
2.4776-2.60810.28811600.19972477263798
2.6081-2.77140.29381270.20872538266599
2.7714-2.98510.2931360.20042538267499
2.9851-3.2850.2431440.1922523266799
3.285-3.75930.26941480.16872526267499
3.7593-4.73210.17221410.13232523266499
4.7321-26.84820.17561230.15372404252794
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.7312-1.49030.29848.0425-5.95167.64950.09450.4608-0.2117-0.55410.13050.87460.7705-0.1388-0.25240.2612-0.007-0.04490.3461-0.08380.316425.8776-34.5588-24.919
23.05680.6125-0.81363.1048-0.89584.2991-0.11550.08670.13160.05680.25060.27480.1016-0.1825-0.1440.13310.0159-0.00140.21660.03420.170329.613-23.6876-19.3343
33.9352-1.0558-0.05672.9669-0.82165.958-0.2551-0.4868-0.02430.32170.15370.08930.49690.26440.12130.13960.0087-0.00190.22080.01190.202335.0438-30.941-12.4981
42.88470.1628-1.43213.1667-0.60614.4394-0.0146-0.0380.17290.05760.13040.1444-0.14930.0493-0.12540.11220.0374-0.0130.21310.01610.177431.1334-22.6662-21.4705
53.5421.24061.40077.08365.91949.8410.05230.2447-0.00370.1564-0.3383-0.4033-0.31340.41980.2910.26060.0015-0.0170.22380.10330.356121.2038-1.012-48.5409
62.63490.10390.47122.4616-0.94613.4270.2930.0229-0.49670.2574-0.035-0.22290.26680.1475-0.2270.30090.0094-0.04440.13880.0010.34513.322-9.0223-43.0726
72.3325-0.9634-0.93181.79410.82296.6158-0.0881-0.0764-0.07720.21250.0484-0.1891-0.4819-0.16870.01750.1812-0.0107-0.02310.11990.02070.241311.2966-0.5476-36.3207
83.0286-0.74711.2441.44150.34214.657-0.02660.2013-0.23250.12150.00390.05870.11-0.1211-0.00060.2385-0.0032-0.01620.11320.04430.314811.3133-9.5551-45.2737
92.44080.2269-0.45772.7819-0.83523.16780.1648-0.20250.25210.1795-0.0207-0.0738-0.44190.1068-0.13880.2184-0.00420.04810.1376-0.03280.2328-0.2141-35.4419-45.1372
103.0904-1.34712.22112.504-0.91566.85020.23760.37130.0869-0.3102-0.2805-0.0879-0.07290.43140.09330.2128-0.01250.06030.1597-0.00850.28591.2689-41.4775-55.2777
112.65190.8413-1.00674.3693-2.62624.86540.1351-0.0252-0.04270.05260.10190.163-0.0732-0.1852-0.32960.1860.02810.03650.1569-0.00440.244-5.5429-37.4672-43.7586
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain C and (resid 48 through 75 )C0
2X-RAY DIFFRACTION2chain C and (resid 76 through 121 )C0
3X-RAY DIFFRACTION3chain C and (resid 122 through 177 )C0
4X-RAY DIFFRACTION4chain C and (resid 178 through 230 )C0
5X-RAY DIFFRACTION5chain B and (resid 48 through 75 )B0
6X-RAY DIFFRACTION6chain B and (resid 76 through 121 )B0
7X-RAY DIFFRACTION7chain B and (resid 122 through 177 )B0
8X-RAY DIFFRACTION8chain B and (resid 178 through 230 )B0
9X-RAY DIFFRACTION9chain A and (resid 47 through 121 )A0
10X-RAY DIFFRACTION10chain A and (resid 122 through 183 )A0
11X-RAY DIFFRACTION11chain A and (resid 184 through 230 )A0

+
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