[English] 日本語
Yorodumi
- PDB-6ai0: Structure of the 328-692 fragment of FlhA (orthorhombic form) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ai0
TitleStructure of the 328-692 fragment of FlhA (orthorhombic form)
ComponentsFlagellar biosynthesis protein FlhA
KeywordsPROTEIN TRANSPORT / flagellar type III secretion
Function / homology
Function and homology information


bacterial-type flagellum assembly / protein secretion / plasma membrane
Similarity search - Function
Flagellar biosynthesis protein FlhA / FHIPEP family, domain 1 / FHIPEP, domain 1 / FHIPEP conserved site / Bacterial export FHIPEP family signature. / Type III secretion system FHIPEP / FHIPEP, domain 3 / FHIPEP, domain 4 / FHIPEP family / Glutaredoxin ...Flagellar biosynthesis protein FlhA / FHIPEP family, domain 1 / FHIPEP, domain 1 / FHIPEP conserved site / Bacterial export FHIPEP family signature. / Type III secretion system FHIPEP / FHIPEP, domain 3 / FHIPEP, domain 4 / FHIPEP family / Glutaredoxin / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Flagellar biosynthesis protein FlhA
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsOgawa, Y. / Kinoshita, M. / Minamino, T. / Imada, K.
Funding support Japan, 6items
OrganizationGrant numberCountry
Japan Society for the Promotion of ScienceJP15H02386 Japan
Japan Society for the Promotion of ScienceJP26293097 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)JP23115008 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)JP24117004 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)JP25121718 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)JP15H01640 Japan
CitationJournal: Structure / Year: 2019
Title: Structural Insights into the Substrate Specificity Switch Mechanism of the Type III Protein Export Apparatus.
Authors: Inoue, Y. / Ogawa, Y. / Kinoshita, M. / Terahara, N. / Shimada, M. / Kodera, N. / Ando, T. / Namba, K. / Kitao, A. / Imada, K. / Minamino, T.
History
DepositionAug 21, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 20, 2019Provider: repository / Type: Initial release
Revision 1.1May 15, 2019Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jun 19, 2019Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Flagellar biosynthesis protein FlhA
B: Flagellar biosynthesis protein FlhA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,7007
Polymers81,3432
Non-polymers3575
Water3,027168
1
A: Flagellar biosynthesis protein FlhA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,8704
Polymers40,6721
Non-polymers1983
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area380 Å2
ΔGint2 kcal/mol
Surface area16780 Å2
MethodPISA
2
B: Flagellar biosynthesis protein FlhA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,8303
Polymers40,6721
Non-polymers1582
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area360 Å2
ΔGint4 kcal/mol
Surface area17400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.920, 93.080, 187.060
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Flagellar biosynthesis protein FlhA


Mass: 40671.645 Da / Num. of mol.: 2 / Fragment: cytoplasmic fragment, residues 328-692
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: flhA, STM1913 / Plasmid: pGEX6p1
Production host: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Strain (production host): SJW1368 / References: UniProt: P40729
#2: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 168 / 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: 2.83 Å3/Da / Density % sol: 56.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1M HEPES NaOH pH 7.5, 10% (w/v) PEG-8000, 0.4M Ca(OAc)2

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jul 5, 2012
RadiationMonochromator: Double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→66 Å / Num. obs: 36660 / % possible obs: 99 % / Redundancy: 7.2 % / Biso Wilson estimate: 37 Å2 / Rmerge(I) obs: 0.119 / Net I/σ(I): 10
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 7 % / Rmerge(I) obs: 0.421 / Mean I/σ(I) obs: 3.4 / Num. unique obs: 3767 / % possible all: 99

-
Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
MOSFLMdata reduction
Aimlessdata scaling
PDB_EXTRACT3.24data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3A5I

3a5i


Resolution: 2.4→41.281 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 30.47
RfactorNum. reflection% reflection
Rfree0.2769 1871 5.11 %
Rwork0.2406 --
obs0.2424 36579 98.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 87.71 Å2 / Biso mean: 48.7591 Å2 / Biso min: 18.92 Å2
Refinement stepCycle: final / Resolution: 2.4→41.281 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5170 0 19 168 5357
Biso mean--44.04 46.39 -
Num. residues----668
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035272
X-RAY DIFFRACTIONf_angle_d0.5887157
X-RAY DIFFRACTIONf_chiral_restr0.043840
X-RAY DIFFRACTIONf_plane_restr0.004937
X-RAY DIFFRACTIONf_dihedral_angle_d3.9633221
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4-2.46490.37611280.3252601272999
2.4649-2.53740.3481490.31392592274197
2.5374-2.61930.38561370.31552635277299
2.6193-2.71290.34811460.30612604275098
2.7129-2.82150.35831360.29712651278798
2.8215-2.94990.28061410.29172619276099
2.9499-3.10540.36551390.27692662280199
3.1054-3.29980.29221340.28132686282099
3.2998-3.55450.30351450.24192669281499
3.5545-3.9120.25271700.23142655282599
3.912-4.47740.22671580.20212708286699
4.4774-5.63880.25981340.202727592893100
5.6388-41.28710.20521540.19032867302199

+
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