[English] 日本語
Yorodumi
- PDB-3njt: Crystal structure of the R450A mutant of the membrane protein FhaC -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3njt
TitleCrystal structure of the R450A mutant of the membrane protein FhaC
ComponentsFilamentous hemagglutinin transporter protein fhaC
KeywordsPROTEIN TRANSPORT / Membrane protein / beta barrel / Omp85/TpsB transporter family
Function / homology
Function and homology information


type V protein secretion system complex / protein secretion by the type V secretion system / porin activity / pore complex / protein transmembrane transporter activity / monoatomic ion transport / cell outer membrane
Similarity search - Function
Two partner secretion pathway transporter / ShlB, POTRA domain / POTRA domain / Haemolysin activator HlyB, C-terminal / Haemolysin secretion/activation protein ShlB/FhaC/HecB / Polypeptide-transport-associated, ShlB-type / POTRA domain, ShlB-type / membrane protein fhac: a member of the omp85/tpsb transporter family / membrane protein fhac / POTRA domain ...Two partner secretion pathway transporter / ShlB, POTRA domain / POTRA domain / Haemolysin activator HlyB, C-terminal / Haemolysin secretion/activation protein ShlB/FhaC/HecB / Polypeptide-transport-associated, ShlB-type / POTRA domain, ShlB-type / membrane protein fhac: a member of the omp85/tpsb transporter family / membrane protein fhac / POTRA domain / POTRA domain profile. / Porin / Ubiquitin-like (UB roll) / Roll / Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Filamentous hemagglutinin transporter protein FhaC
Similarity search - Component
Biological speciesBordetella pertussis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsClantin, B. / Delattre, A.S. / Jacob-Dubuisson, F. / Villeret, V.
CitationJournal: Febs J. / Year: 2010
Title: Functional importance of a conserved sequence motif in FhaC, a prototypic member of the TpsB/Omp85 superfamily.
Authors: Delattre, A.S. / Clantin, B. / Saint, N. / Locht, C. / Villeret, V. / Jacob-Dubuisson, F.
History
DepositionJun 18, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 3, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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: Filamentous hemagglutinin transporter protein fhaC


Theoretical massNumber of molelcules
Total (without water)62,5981
Polymers62,5981
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)107.550, 139.390, 113.080
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein Filamentous hemagglutinin transporter protein fhaC / TpsB transporter


Mass: 62598.031 Da / Num. of mol.: 1 / Fragment: UNP residues 34-584 / Mutation: R450A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella pertussis (bacteria) / Strain: Tohama 1 / Gene: fhaC, BP1884 / Plasmid: pFJD118-R450A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 OMP5 / References: UniProt: P35077

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.39 Å3/Da / Density % sol: 63.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 28% PEG 1000, 1% B-octyl-glucoside, 500 mM imidazole pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 3.5→48.6 Å / Num. obs: 11007 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Redundancy: 14.5 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 30
Reflection shellResolution: 3.5→3.6 Å / Redundancy: 14.9 % / Rmerge(I) obs: 0.282 / Mean I/σ(I) obs: 6.1 / % possible all: 100

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
CNSrefinement
XDSdata reduction
XDSdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2GDZ

2gdz


Resolution: 3.5→48.56 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 5589898 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.38 1113 10.1 %RANDOM
Rwork0.35 ---
obs0.35 11007 99.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 106.488 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 105.5 Å2
Baniso -1Baniso -2Baniso -3
1-39.04 Å20 Å20 Å2
2---21.59 Å20 Å2
3----17.45 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.55 Å0.53 Å
Luzzati d res low-5 Å
Luzzati sigma a0.94 Å1.06 Å
Refinement stepCycle: LAST / Resolution: 3.5→48.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3514 0 0 0 3514
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg2.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d29
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.98
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: NONE
Xplor fileSerial no: 1 / Param file: protein_rep.param / Topol file: protein.top

+
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