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- PDB-6gox: SecA -

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Basic information

Entry
Database: PDB / ID: 6gox
TitleSecA
ComponentsProtein translocase subunit SecA
KeywordsPROTEIN TRANSPORT / truncation
Function / homology
Function and homology information


preprotein binding / cell envelope Sec protein transport complex / protein-exporting ATPase activity / protein-secreting ATPase / protein transport by the Sec complex / intracellular protein transmembrane transport / protein import / protein targeting to membrane / protein secretion / protein targeting ...preprotein binding / cell envelope Sec protein transport complex / protein-exporting ATPase activity / protein-secreting ATPase / protein transport by the Sec complex / intracellular protein transmembrane transport / protein import / protein targeting to membrane / protein secretion / protein targeting / ribonucleoprotein complex binding / chaperone-mediated protein folding / cytoplasmic side of plasma membrane / ribosome binding / protein transport / zinc ion binding / ATP binding / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
SecA P-loop domain / SEC-C motif / 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 P-loop domain / SEC-C motif / 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 / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Protein translocase subunit SecA
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.5 Å
AuthorsWhite, S.A. / Huber, D.
CitationJournal: Elife / Year: 2019
Title: The C-terminal tail of the bacterial translocation ATPase SecA modulates its activity.
Authors: Jamshad, M. / Knowles, T.J. / White, S.A. / Ward, D.G. / Mohammed, F. / Rahman, K.F. / Wynne, M. / Hughes, G.W. / Kramer, G. / Bukau, B. / Huber, D.
History
DepositionJun 4, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 19, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Jul 1, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein translocase subunit SecA


Theoretical massNumber of molelcules
Total (without water)93,3511
Polymers93,3511
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area39380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)163.140, 106.830, 75.980
Angle α, β, γ (deg.)90.000, 102.810, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Protein translocase subunit SecA


Mass: 93351.031 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: secA, azi, pea, prlD, b0098, JW0096 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P10408

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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: 3.46 Å3/Da / Density % sol: 64.43 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 18% PEG 3350, 0.054 BIS-TRIS propane, pH6.4, 0.036M citrate, plus additives
PH range: 6.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.5→88.69 Å / Num. obs: 31379 / % possible obs: 99.4 % / Redundancy: 3.45 % / Net I/σ(I): 9.44
Reflection shellResolution: 3.5→3.71 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
REFMAC5.8.0107refinement
PDB_EXTRACT3.24data extraction
PHASERphasing
RefinementResolution: 3.5→88.69 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.889 / SU B: 40.702 / SU ML: 0.607 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.662
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2927 785 4.9 %RANDOM
Rwork0.2315 ---
obs0.2344 15321 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 326.58 Å2 / Biso mean: 157.574 Å2 / Biso min: 75.58 Å2
Baniso -1Baniso -2Baniso -3
1--6.54 Å2-0 Å2-4.27 Å2
2--4.7 Å20 Å2
3---3.43 Å2
Refinement stepCycle: final / Resolution: 3.5→88.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6182 0 0 0 6182
Num. residues----777
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0196283
X-RAY DIFFRACTIONr_bond_other_d0.0030.026109
X-RAY DIFFRACTIONr_angle_refined_deg1.4611.9658475
X-RAY DIFFRACTIONr_angle_other_deg1.123314032
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.895773
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.15824.097310
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.2151160
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9871556
X-RAY DIFFRACTIONr_chiral_restr0.0780.2944
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027092
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021412
LS refinement shellResolution: 3.5→3.591 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 69 -
Rwork0.352 1095 -
all-1164 -
obs--99.83 %

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