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- PDB-9e0s: Cryo-EM structure of a the periplasmic insert from Myxococcus TAtC -

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Basic information

Entry
Database: PDB / ID: 9e0s
TitleCryo-EM structure of a the periplasmic insert from Myxococcus TAtC
ComponentsSec-independent protein translocase protein TatC
KeywordsTRANSLOCASE / Membrane Protein / TatC / TatB / twin-arginine translocation
Function / homologySec-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 speciesMyxococcus xanthus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.98 Å
AuthorsDeme, J.C. / Bryant, O.J. / Berks, B.C. / Lea, S.M.
Funding support United Kingdom, United States, 3items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/L000776/1 United Kingdom
Wellcome Trust107929/Z/15/Z United Kingdom
National Institutes of Health/National Cancer Institute (NIH/NCI)Intramural Research Program United States
CitationJournal: To Be Published
Title: Structure of the twin-arginine protein translocation pathway core complex and the molecular basis for substrate recognition
Authors: Deme, J.C. / Bryant, O.J. / Berks, B.C. / Lea, S.M.
History
DepositionOct 18, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 27, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sec-independent protein translocase protein TatC
B: Sec-independent protein translocase protein TatC
C: Sec-independent protein translocase protein TatC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,0984
Polymers61,0023
Non-polymers961
Water5,783321
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6160 Å2
ΔGint-34 kcal/mol
Surface area26780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.776, 110.776, 101.898
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number89
Space group name H-MP422
Space group name HallP42
Symmetry operation#1: x,y,z
#2: -y,x,z
#3: y,-x,z
#4: x,-y,-z
#5: -x,y,-z
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
Components on special symmetry positions
IDModelComponents
11B-320-

HOH

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Components

#1: Protein Sec-independent protein translocase protein TatC


Mass: 20333.949 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Myxococcus xanthus (bacteria) / Gene: tatC, N3T43_29770 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2PHA2
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 321 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.56 Å3/Da / Density % sol: 52 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / Details: lithium sulphate, Tris pH 8.5, PEG 8000, PEG 1000

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Data collection

DiffractionMean temperature: 120 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS 12M / Detector: PIXEL / Date: Oct 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.98→62.1 Å / Num. obs: 44477 / % possible obs: 100 % / Redundancy: 25.2 % / Biso Wilson estimate: 25.61 Å2 / Rpim(I) all: 0.054 / Net I/σ(I): 11.7
Reflection shellResolution: 1.98→2.03 Å / Redundancy: 25.6 % / Mean I/σ(I) obs: 1.7 / Num. unique obs: 3065 / Rsym value: 0.521 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIXdev_5278refinement
MOSFLMdata reduction
SCALAdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.98→62.1 Å / SU ML: 0.2229 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.9354
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2235 2271 5.11 %
Rwork0.1873 42188 -
obs0.1892 44459 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.37 Å2
Refinement stepCycle: LAST / Resolution: 1.98→62.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4040 0 5 321 4366
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00634092
X-RAY DIFFRACTIONf_angle_d0.73965511
X-RAY DIFFRACTIONf_chiral_restr0.0379621
X-RAY DIFFRACTIONf_plane_restr0.0089727
X-RAY DIFFRACTIONf_dihedral_angle_d13.92341514
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.98-2.030.32781160.2722584X-RAY DIFFRACTION99.96
2.03-2.070.28631460.2432584X-RAY DIFFRACTION100
2.07-2.130.28551360.21852612X-RAY DIFFRACTION99.96
2.13-2.180.25341530.21322573X-RAY DIFFRACTION99.96
2.18-2.250.30021320.20552605X-RAY DIFFRACTION100
2.25-2.320.25371290.20282616X-RAY DIFFRACTION99.96
2.32-2.40.22451470.18472582X-RAY DIFFRACTION99.96
2.4-2.50.24631370.18312630X-RAY DIFFRACTION100
2.5-2.610.27271470.18442596X-RAY DIFFRACTION99.96
2.61-2.750.23121570.18892615X-RAY DIFFRACTION100
2.75-2.920.24271040.19252678X-RAY DIFFRACTION100
2.92-3.150.23611490.19822625X-RAY DIFFRACTION100
3.15-3.470.20411600.17982642X-RAY DIFFRACTION100
3.47-3.970.20961490.16992680X-RAY DIFFRACTION100
3.97-50.17461330.15462716X-RAY DIFFRACTION100
5-62.10.18631760.18982850X-RAY DIFFRACTION99.74

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