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- PDB-3dl8: Structure of the complex of aquifex aeolicus SecYEG and bacillus ... -

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Basic information

Entry
Database: PDB / ID: 3dl8
TitleStructure of the complex of aquifex aeolicus SecYEG and bacillus subtilis SecA
Components
  • Preprotein translocase subunit secY
  • Protein translocase subunit secA
  • Protein-export membrane protein secG
  • SecE
KeywordsPROTEIN TRANSPORT / RecA-type ATPase membrane protein translocation Protein-protein complex / ATP-binding / Cell membrane / Membrane / Metal-binding / Nucleotide-binding / Translocation / Transport / Transmembrane
Function / homology
Function and homology information


cell envelope Sec protein transport complex / protein-exporting ATPase activity / protein-secreting ATPase / protein transport by the Sec complex / intracellular protein transmembrane transport / protein-transporting ATPase activity / protein import / SRP-dependent cotranslational protein targeting to membrane, translocation / signal sequence binding / plasma membrane => GO:0005886 ...cell envelope Sec protein transport complex / protein-exporting ATPase activity / protein-secreting ATPase / protein transport by the Sec complex / intracellular protein transmembrane transport / protein-transporting ATPase activity / protein import / SRP-dependent cotranslational protein targeting to membrane, translocation / signal sequence binding / plasma membrane => GO:0005886 / protein transmembrane transporter activity / protein secretion / protein targeting / membrane => GO:0016020 / membrane raft / ATP binding / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
Preprotein translocase SecG subunit / Preprotein translocase SecG subunit / SecA P-loop domain / SEC-C motif / SecE subunit of protein translocation complex, bacterial-like / SecE superfamily / SEC-C motif / SecA, C-terminal helicase domain / Protein translocase subunit SecA / SecA DEAD-like, N-terminal ...Preprotein translocase SecG subunit / Preprotein translocase SecG subunit / SecA P-loop domain / SEC-C motif / SecE subunit of protein translocation complex, bacterial-like / SecE superfamily / SEC-C motif / SecA, C-terminal helicase domain / Protein translocase subunit SecA / SecA DEAD-like, N-terminal / SecA Wing/Scaffold / SecA, preprotein cross-linking domain / SecA motor DEAD / SecA conserved site / SecA, Wing/Scaffold superfamily / SecA, preprotein cross-linking domain superfamily / SecA preprotein cross-linking domain / SecA Wing and Scaffold domain / SecA DEAD-like domain / SecA family signature. / SecA family profile. / SecA DEAD-like domain / SecA preprotein cross-linking domain / Protein translocase subunit SecY / Protein secY signature 1. / 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 / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Protein translocase subunit SecE / Protein translocase subunit SecY / Protein-export membrane protein SecG / Protein translocase subunit SecA
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
Aquifex aeolicus (bacteria)
Aquifex Aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 7.5 Å
AuthorsNam, Y. / Zimmer, J. / Rapoport, T.A.
CitationJournal: Nature / Year: 2008
Title: Structure of a complex of the ATPase SecA and the protein-translocation channel.
Authors: Zimmer, J. / Nam, Y. / Rapoport, T.A.
History
DepositionJun 26, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 2, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 25, 2013Group: Derived calculations
Revision 1.3Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

Downloads & links

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Assembly

Deposited unit
A: Protein translocase subunit secA
B: Protein translocase subunit secA
G: Preprotein translocase subunit secY
H: Preprotein translocase subunit secY
C: SecE
D: SecE
E: Protein-export membrane protein secG
F: Protein-export membrane protein secG


Theoretical massNumber of molelcules
Total (without water)311,6118
Polymers311,6118
Non-polymers00
Water0
1
A: Protein translocase subunit secA
G: Preprotein translocase subunit secY
C: SecE
E: Protein-export membrane protein secG


Theoretical massNumber of molelcules
Total (without water)155,8054
Polymers155,8054
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein translocase subunit secA
H: Preprotein translocase subunit secY
D: SecE
F: Protein-export membrane protein secG


Theoretical massNumber of molelcules
Total (without water)155,8054
Polymers155,8054
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)146.359, 167.974, 187.722
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Protein translocase subunit secA


Mass: 88803.023 Da / Num. of mol.: 2 / Fragment: UNP residues 1-779
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: secA, div+, BSU35300 / Production host: Escherichia coli (E. coli) / References: UniProt: P28366
#2: Protein Preprotein translocase subunit secY


Mass: 48139.977 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Gene: secY, aq_079 / Production host: Escherichia coli (E. coli) / References: UniProt: O66491
#3: Protein SecE


Mass: 7504.100 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex Aeolicus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: D0VWU4*PLUS
#4: Protein Protein-export membrane protein secG


Mass: 11358.197 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Gene: secG, aq_098 / Production host: Escherichia coli (E. coli) / References: UniProt: O66505

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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: 3.7 Å3/Da / Density % sol: 67.88 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 26-28% (w/v) PEG 3350 and 250mM lithium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 23, 2007
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 7.5→15 Å / Num. all: 5443 / Num. obs: 5416 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 7.5→7.9 Å / % possible all: 99

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Processing

Software
NameVersionClassificationNB
CNS1.2refinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 7.5→14.99 Å / Rfactor Rfree error: 0.017 / Occupancy max: 1 / Occupancy min: 1 / Data cutoff high absF: 3033230 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: BULK SOLVENT MODEL USED. MODEL CONTAINS BACKBONE ONLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.39 532 9.8 %RANDOM
Rwork0.365 ---
all0.367 5446 --
obs0.367 5416 99.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 234.636 Å2 / ksol: 0.25 e/Å3
Displacement parametersBiso max: 580.7 Å2 / Biso mean: 401.742 Å2 / Biso min: 229.26 Å2
Baniso -1Baniso -2Baniso -3
1-33.98 Å20 Å20 Å2
2--38.18 Å20 Å2
3----72.16 Å2
Refine analyze
FreeObs
Luzzati coordinate error1.9 Å1.6 Å
Luzzati d res low-15 Å
Luzzati sigma a1.47 Å1.47 Å
Refinement stepCycle: LAST / Resolution: 7.5→14.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10232 0 0 0 10232
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.035
X-RAY DIFFRACTIONc_angle_deg2.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.3
X-RAY DIFFRACTIONc_improper_angle_d1.96
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 7.5→7.9 Å / Rfactor Rfree error: 0.055 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.447 67 7.5 %
Rwork0.444 826 -
all-893 -
obs--99 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2

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