[English] 日本語
Yorodumi
- PDB-3vki: Monoclinic Crystal Structure of Salmonella FlgA in closed form -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3vki
TitleMonoclinic Crystal Structure of Salmonella FlgA in closed form
ComponentsFlagella basal body P-ring formation protein flgA
KeywordsCHAPERONE / BACTERIAL FLAGELLUM / SECRETION / DISULFIDE BOND
Function / homology
Function and homology information


bacterial-type flagellum assembly / bacterial-type flagellum-dependent cell motility / periplasmic space
Similarity search - Function
SH3 type barrels. - #760 / Flagella basal body P-ring formation protein FlgA, C-terminal / Flagellar protein FlgA / Chaperone for flagella basal body P-ring formation / SAF domain / SAF / SAF domain / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
Flagella basal body P-ring formation protein FlgA
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsMatsunami, H. / Samatey, F.A. / Namba, K.
CitationJournal: Sci Rep / Year: 2016
Title: Structural flexibility of the periplasmic protein, FlgA, regulates flagellar P-ring assembly in Salmonella enterica
Authors: Matsunami, H. / Yoon, Y.H. / Meshcheryakov, V.A. / Namba, K. / Samatey, F.A.
History
DepositionNov 16, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 21, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 6, 2016Group: Database references
Revision 1.2Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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: Flagella basal body P-ring formation protein flgA
B: Flagella basal body P-ring formation protein flgA
C: Flagella basal body P-ring formation protein flgA
D: Flagella basal body P-ring formation protein flgA


Theoretical massNumber of molelcules
Total (without water)94,6234
Polymers94,6234
Non-polymers00
Water3,351186
1
A: Flagella basal body P-ring formation protein flgA


Theoretical massNumber of molelcules
Total (without water)23,6561
Polymers23,6561
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Flagella basal body P-ring formation protein flgA


Theoretical massNumber of molelcules
Total (without water)23,6561
Polymers23,6561
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Flagella basal body P-ring formation protein flgA


Theoretical massNumber of molelcules
Total (without water)23,6561
Polymers23,6561
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Flagella basal body P-ring formation protein flgA


Theoretical massNumber of molelcules
Total (without water)23,6561
Polymers23,6561
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.926, 103.317, 85.501
Angle α, β, γ (deg.)90.000, 107.260, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Flagella basal body P-ring formation protein flgA / Flagellar flga protein


Mass: 23655.721 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: SJW1103 / Gene: flgA / Plasmid: PET22B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P40131
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48.83 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 12% PEG 6000, 0.05M CITRIC ACID PH 4.2, 1.0M LICl, 14% 2-METHYL-2,4-PENTANEDIOL, vapor diffusion, hanging drop, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: May 19, 2011
RadiationMonochromator: DOUBLE-CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→40.8 Å / Num. obs: 39534 / % possible obs: 99.3 %
Reflection shellResolution: 2.3→2.42 Å / % possible all: 96.4

-
Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALACCP4_3.3.16data scaling
PHENIX1.7.2_869refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→25 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7739 / SU ML: 0.86 / σ(F): 0 / Phase error: 29.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2812 1983 5.02 %RANDOM
Rwork0.2513 ---
obs0.2529 39492 99.26 %-
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.642 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 143.44 Å2 / Biso mean: 60.0246 Å2 / Biso min: 5.08 Å2
Baniso -1Baniso -2Baniso -3
1-11.3415 Å2-0 Å2-0.8884 Å2
2---11.4207 Å2-0 Å2
3---0.0792 Å2
Refinement stepCycle: LAST / Resolution: 2.3→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5980 0 0 186 6166
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046064
X-RAY DIFFRACTIONf_angle_d0.9698240
X-RAY DIFFRACTIONf_chiral_restr0.075968
X-RAY DIFFRACTIONf_plane_restr0.0031100
X-RAY DIFFRACTIONf_dihedral_angle_d16.6782248
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.35750.33271510.30242491264293
2.3575-2.42120.37991470.30212646279399
2.4212-2.49240.29221290.305327002829100
2.4924-2.57270.39161320.288427262858100
2.5727-2.66460.34751390.288126542793100
2.6646-2.77110.31221480.270726912839100
2.7711-2.89710.31911320.253926942826100
2.8971-3.04960.28321660.262527002866100
3.0496-3.24030.28281350.258126852820100
3.2403-3.48980.26631480.251326722820100
3.4898-3.83990.29521460.241727262872100
3.8399-4.39290.24971430.222427032846100
4.3929-5.52470.23061290.223927302859100
5.5247-24.98560.26091380.25122691282997

+
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