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- PDB-5ch4: Peptide-Bound State of Thermus thermophilus SecYEG -

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Basic information

Entry
Database: PDB / ID: 5ch4
TitlePeptide-Bound State of Thermus thermophilus SecYEG
Components
  • Protein translocase subunit SecE
  • Protein translocase subunit SecY
  • Putative preprotein translocase, SecG subunit
KeywordsPROTEIN TRANSPORT / translocon / membrane protein
Function / homology
Function and homology information


protein transport by the Sec complex / intracellular protein transmembrane transport / protein-transporting ATPase activity / protein secretion / protein transmembrane transporter activity / protein targeting / plasma membrane
Similarity search - Function
Preprotein translocase SecY subunit / SecY subunit domain / Preprotein translocase SecG subunit / Preprotein translocase SecG subunit / SecE subunit of protein translocation complex, bacterial-like / SecE superfamily / Protein translocase subunit SecY / Protein secE/sec61-gamma signature. / Protein secY signature 2. / SecE/Sec61-gamma subunits of protein translocation complex ...Preprotein translocase SecY subunit / SecY subunit domain / Preprotein translocase SecG subunit / Preprotein translocase SecG subunit / SecE subunit of protein translocation complex, bacterial-like / SecE superfamily / Protein translocase subunit SecY / Protein secE/sec61-gamma signature. / Protein secY signature 2. / SecE/Sec61-gamma subunits of protein translocation complex / Protein translocase complex, SecE/Sec61-gamma subunit / SecY/SEC61-alpha family / SecY domain superfamily / SecY conserved site / SecY / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Protein translocase subunit SecE / Protein-export membrane protein SecG / Protein translocase subunit SecY
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.64 Å
AuthorsTanaka, Y. / Sugano, Y. / Takemoto, M. / Kusakizako, T. / Kumazaki, K. / Ishitani, R. / Nureki, O. / Tsukazaki, T.
CitationJournal: Cell Rep / Year: 2015
Title: Crystal Structures of SecYEG in Lipidic Cubic Phase Elucidate a Precise Resting and a Peptide-Bound State.
Authors: Tanaka, Y. / Sugano, Y. / Takemoto, M. / Mori, T. / Furukawa, A. / Kusakizako, T. / Kumazaki, K. / Kashima, A. / Ishitani, R. / Sugita, Y. / Nureki, O. / Tsukazaki, T.
History
DepositionJul 10, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 25, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 23, 2015Group: Database references
Revision 1.2Feb 19, 2020Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 8, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
Y: Protein translocase subunit SecY
E: Protein translocase subunit SecE
G: Putative preprotein translocase, SecG subunit


Theoretical massNumber of molelcules
Total (without water)63,5323
Polymers63,5323
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7540 Å2
ΔGint-64 kcal/mol
Surface area26450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.829, 138.007, 115.974
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Protein translocase subunit SecY


Mass: 48515.910 Da / Num. of mol.: 1 / Mutation: L2V, K248G, V249A, V250A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / Gene: secY, TTHA1672
Production host: Escherichia coli BL21-Gold(DE3)pLysS AG (bacteria)
References: UniProt: Q5SHQ8
#2: Protein Protein translocase subunit SecE


Mass: 7072.410 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / Gene: secE, TTHA0249
Production host: Escherichia coli BL21-Gold(DE3)pLysS AG (bacteria)
References: UniProt: P38383
#3: Protein Putative preprotein translocase, SecG subunit


Mass: 7943.501 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 43-117
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / Gene: TTHA1784
Production host: Escherichia coli BL21-Gold(DE3)pLysS AG (bacteria)
References: UniProt: Q5SHE6

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.09 Å3/Da / Density % sol: 60.17 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 7.5 / Details: PEG 500DME, ZnSO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jul 18, 2014
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.6→50 Å / Num. obs: 9099 / % possible obs: 99.8 % / Redundancy: 7.4 % / Net I/σ(I): 5.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata collection
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZJS

2zjs


Resolution: 3.64→44.393 Å / SU ML: 0.51 / Cross valid method: NONE / σ(F): 1.36 / Phase error: 30.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.279 908 10 %
Rwork0.2541 --
obs0.2567 9079 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.64→44.393 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4238 0 0 0 4238
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024349
X-RAY DIFFRACTIONf_angle_d0.5775927
X-RAY DIFFRACTIONf_dihedral_angle_d10.4341507
X-RAY DIFFRACTIONf_chiral_restr0.022707
X-RAY DIFFRACTIONf_plane_restr0.003740
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.6395-3.86740.35961500.351348X-RAY DIFFRACTION99
3.8674-4.16590.38051450.28531327X-RAY DIFFRACTION100
4.1659-4.58470.26551500.27331345X-RAY DIFFRACTION100
4.5847-5.24720.29211510.24671360X-RAY DIFFRACTION100
5.2472-6.60740.31861520.27431365X-RAY DIFFRACTION100
6.6074-44.39660.21041600.20411426X-RAY DIFFRACTION99

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