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- PDB-2zqp: Crystal Structure of SecYE translocon from Thermus thermophilus -

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Basic information

Entry
Database: PDB / ID: 2zqp
TitleCrystal Structure of SecYE translocon from Thermus thermophilus
Components
  • Preprotein translocase SecE subunit
  • Preprotein translocase SecY subunit
KeywordsPROTEIN TRANSPORT / TRANSLOCON / SEC / PROTEIN-CONDUCTING-CHANNEL / Membrane / Translocation / Transmembrane / Transport
Function / homology
Function and homology information


protein transport by the Sec complex / intracellular protein transmembrane transport / protein transmembrane transporter activity / protein secretion / protein targeting / plasma membrane
Similarity search - Function
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
Similarity search - Domain/homology
Protein translocase subunit SecE / Protein translocase subunit SecY / Protein translocase subunit SecY / Protein translocase subunit SecE
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 6 Å
AuthorsTsukazaki, T. / Nureki, O.
CitationJournal: Nature / Year: 2008
Title: Conformational transition of Sec machinery inferred from bacterial SecYE structures
Authors: Tsukazaki, T. / Mori, H. / Fukai, S. / Ishitani, R. / Mori, T. / Dohmae, N. / Perederina, A. / Sugita, Y. / Vassylyev, D.G. / Ito, K. / Nureki, O.
History
DepositionAug 14, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 14, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
Y: Preprotein translocase SecY subunit
E: Preprotein translocase SecE subunit


Theoretical massNumber of molelcules
Total (without water)54,7162
Polymers54,7162
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3540 Å2
ΔGint-33 kcal/mol
Surface area25640 Å2
MethodPISA
2
Y: Preprotein translocase SecY subunit
E: Preprotein translocase SecE subunit

Y: Preprotein translocase SecY subunit
E: Preprotein translocase SecE subunit


Theoretical massNumber of molelcules
Total (without water)109,4314
Polymers109,4314
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_455-x-1,y,-z1
Buried area10160 Å2
ΔGint-68 kcal/mol
Surface area48200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.876, 91.876, 240.560
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322

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Components

#1: Protein Preprotein translocase SecY subunit


Mass: 47643.102 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-434 / Mutation: L2V, R252G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Plasmid: PTV118N / Production host: Escherichia coli (E. coli) / References: UniProt: Q8KZP3, UniProt: Q5SHQ8*PLUS
#2: Protein Preprotein translocase SecE subunit


Mass: 7072.410 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Plasmid: PTV118N / Production host: Escherichia coli (E. coli) / References: UniProt: Q8KZP4, UniProt: P38383*PLUS

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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: 4.64 Å3/Da / Density % sol: 73.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 28.5% PEG 3350, 0.18M Na-citrate, 0.015% octaethylene glycol monododecyl ether, 5% glycerol, 0.0001M Pefabloc, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 23, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 6→50 Å / Num. obs: 2743 / % possible obs: 93.4 %

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: the SecYE structure produced by MD simulation using 2ZJS structure
Resolution: 6→42.92 Å / Cor.coef. Fo:Fc: 0.783 / Cor.coef. Fo:Fc free: 0.729 / SU B: 436.011 / SU ML: 4.28 / Cross valid method: THROUGHOUT / ESU R Free: 3.246 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.44504 123 4.5 %RANDOM
Rwork0.40704 ---
obs0.40884 2616 93.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 368.097 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å20 Å20 Å2
2--0.31 Å20 Å2
3----0.63 Å2
Refinement stepCycle: LAST / Resolution: 6→42.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3594 0 0 0 3594
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0223680
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.421.9685009
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5155458
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.28522.397146
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.68915590
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1151526
X-RAY DIFFRACTIONr_chiral_restr0.0880.2591
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022741
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2760.22336
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3230.22501
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2340.2171
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4940.2169
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1910.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.1391.52373
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.24623679
X-RAY DIFFRACTIONr_scbond_it0.25531531
X-RAY DIFFRACTIONr_scangle_it0.4254.51330
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 5.998→6.153 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.389 10 -
Rwork0.287 168 -
obs--83.57 %

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