[English] 日本語
Yorodumi
- PDB-4hts: Crystal Structure of Twin Arginine Translocase Receptor- TatC -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4hts
TitleCrystal Structure of Twin Arginine Translocase Receptor- TatC
ComponentsSec-independent protein translocase protein TatC
KeywordsPROTEIN TRANSPORT / Twin arginine translocase receptor
Function / homologySec-independent periplasmic protein translocase TatC / Sec-independent periplasmic protein translocase, conserved site / Sec-independent protein translocase protein (TatC) / TatC family signature. / proton motive force dependent protein transmembrane transporter activity / TAT protein transport complex / protein transport by the Tat complex / intracellular protein transmembrane transport / Sec-independent protein translocase protein TatC
Function and homology information
Biological speciesAquifex aeolicus VF5 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4 Å
AuthorsRamasamy, S. / Chartron, J.W. / Clemons Jr., W.M.
CitationJournal: Structure / Year: 2013
Title: The Glove-like Structure of the Conserved Membrane Protein TatC Provides Insight into Signal Sequence Recognition in Twin-Arginine Translocation.
Authors: Ramasamy, S. / Abrol, R. / Suloway, C.J. / Clemons, W.M.
History
DepositionNov 1, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2013Provider: repository / Type: Initial release
Revision 1.1May 29, 2013Group: Database references
Revision 1.2Jul 17, 2019Group: Advisory / Data collection / Refinement description / Category: pdbx_unobs_or_zero_occ_residues / software
Item: _software.classification / _software.name / _software.version
Revision 1.3Feb 28, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_residues / 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: Sec-independent protein translocase protein TatC


Theoretical massNumber of molelcules
Total (without water)26,4361
Polymers26,4361
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)109.780, 109.780, 107.020
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122

-
Components

#1: Protein Sec-independent protein translocase protein TatC


Mass: 26436.027 Da / Num. of mol.: 1 / Fragment: UNP residues 1-232 / Mutation: K40A, E41A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus VF5 (bacteria) / Strain: VF5 / Gene: tatC, aq_1267 / Plasmid: pET33b / Production host: Escherichia coli (E. coli) / Strain (production host): BL(21) Gold / References: UniProt: O67305

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 6.2 Å3/Da / Density % sol: 80.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 28% Jeffamine ED-2001 0.05M HEPES pH 7.5 10% Methyl-2,4-pentanediol (MPD)., VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1.08 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 25, 2008
RadiationMonochromator: LIQUID NITROGEN-COOLED DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 4→110.43 Å / Num. obs: 5887 / % possible obs: 99.77 % / Observed criterion σ(F): 22.03 / Observed criterion σ(I): 66.49 / Redundancy: 7.7 % / Rsym value: 0.062 / Net I/σ(I): 16.8
Reflection shell
Resolution (Å)Redundancy (%)Rsym valueDiffraction-ID% possible all
4.1-4.328.10.83199.8
4.32-4.58199.9
4.58-4.9199.7
4.9-5.21100
5.2-5.8199.9
5.8-6.481100
6.49-7.49199.9
7.49-9.171100
9.17-12.971100
12.97-39.04196.3

-
Processing

Software
NameVersionClassification
PHENIX1.8.1_1168refinement
PHASERphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
SCALAdata scaling
Blu-Icedata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 4→29.911 Å / Cor.coef. Fo:Fc: 0.867 / Cor.coef. Fo:Fc free: 0.829 / SU ML: 0.54 / σ(F): 1.91 / Phase error: 39.28 / Stereochemistry target values: ML
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflection
Rfree0.3231 567 9.63 %
Rwork0.2882 --
obs0.2916 5885 99.88 %
all-5585 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 211.998 Å2
Baniso -1Baniso -2Baniso -3
1-1.52 Å20 Å20 Å2
2--1.52 Å20 Å2
3----3.04 Å2
Refinement stepCycle: LAST / Resolution: 4→29.911 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1819 0 0 0 1819
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031868
X-RAY DIFFRACTIONf_angle_d0.8822544
X-RAY DIFFRACTIONf_dihedral_angle_d11.675665
X-RAY DIFFRACTIONf_chiral_restr0.067312
X-RAY DIFFRACTIONf_plane_restr0.004301
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4-4.40140.3581400.3261289X-RAY DIFFRACTION100
4.4014-5.03570.33871510.28191284X-RAY DIFFRACTION100
5.0357-6.33450.35141330.3371329X-RAY DIFFRACTION100
6.3345-29.91220.30041430.26731416X-RAY DIFFRACTION100

+
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://pdbjlc1.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