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- PDB-5aww: Precise Resting State of Thermus thermophilus SecYEG -

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Basic information

Entry
Database: PDB / ID: 5aww
TitlePrecise Resting State of Thermus thermophilus SecYEG
Components
  • Protein translocase subunit SecE
  • Protein translocase subunit SecY
  • Putative preprotein translocase, SecG subunit
KeywordsPROTEIN TRANSPORT/IMMUNE SYSTEM / translocon / membrane protein / PROTEIN TRANSPORT-IMMUNE SYSTEM complex
Function / homology
Function and homology information


protein transport by the Sec complex / intracellular protein transmembrane transport / protein-transporting ATPase activity / protein transmembrane transporter activity / protein secretion / 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
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 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: 2.724 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: PDBJ / Processing site: PDBJ
Revision 1.0Nov 25, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 16, 2015Group: Database references
Revision 1.2Feb 26, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,89514
Polymers63,9733
Non-polymers3,92211
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7980 Å2
ΔGint-63 kcal/mol
Surface area28480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.493, 112.904, 140.002
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Protein translocase subunit SecY


Mass: 48957.516 Da / Num. of mol.: 1 / Mutation: L2V, R252G
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 43-116
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
#4: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C21H40O4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.26 Å3/Da / Density % sol: 62.25 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 6.5 / Details: PEG 500MME, MgSO4, Na2SO4

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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: Jan 20, 2015
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 21452 / % possible obs: 94.5 % / Redundancy: 4.7 % / Net I/σ(I): 10.5

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
HKL-2000data collection
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZJS

2zjs


Resolution: 2.724→43.943 Å / SU ML: 0.4 / Cross valid method: NONE / σ(F): 1.47 / Phase error: 26.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2683 2009 9.37 %
Rwork0.219 --
obs0.2234 21441 94.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.724→43.943 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4348 0 149 7 4504
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034586
X-RAY DIFFRACTIONf_angle_d0.6236182
X-RAY DIFFRACTIONf_dihedral_angle_d10.7681677
X-RAY DIFFRACTIONf_chiral_restr0.023718
X-RAY DIFFRACTIONf_plane_restr0.003765
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7237-2.79180.32191010.28621017X-RAY DIFFRACTION70
2.7918-2.86730.30461540.30051276X-RAY DIFFRACTION89
2.8673-2.95160.3141270.26871380X-RAY DIFFRACTION94
2.9516-3.04690.33791340.25811385X-RAY DIFFRACTION94
3.0469-3.15570.28051540.25651374X-RAY DIFFRACTION95
3.1557-3.2820.29481420.24561407X-RAY DIFFRACTION97
3.282-3.43140.29711410.22741399X-RAY DIFFRACTION96
3.4314-3.61220.26521460.21651426X-RAY DIFFRACTION97
3.6122-3.83840.2741540.20211422X-RAY DIFFRACTION98
3.8384-4.13450.24341450.19951452X-RAY DIFFRACTION98
4.1345-4.55020.27531490.20911449X-RAY DIFFRACTION98
4.5502-5.20780.21741510.18221438X-RAY DIFFRACTION97
5.2078-6.55770.25711510.24041474X-RAY DIFFRACTION98
6.5577-43.94880.25731600.19711533X-RAY DIFFRACTION98

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