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- PDB-4hts: Crystal Structure of Twin Arginine Translocase Receptor- TatC -

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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, conserved site / TatC family signature. / Sec-independent periplasmic protein translocase TatC / Sec-independent protein translocase protein (TatC) / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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

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Experimental details

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Experiment

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

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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

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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

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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

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