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- PDB-6sxh: Crystal structure of the accessory translocation ATPase, SecA2, f... -

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Basic information

Entry
Database: PDB / ID: 6sxh
TitleCrystal structure of the accessory translocation ATPase, SecA2, from Clostridium difficile
ComponentsProtein translocase subunit SecA 2
KeywordsPROTEIN TRANSPORT / SecA2 / ATPase / Pathogenesis
Function / homology
Function and homology information


protein-exporting ATPase activity / protein-secreting ATPase / intracellular protein transmembrane transport / protein import / protein targeting / ATP binding / plasma membrane / cytoplasm
Similarity search - Function
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, 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 superfamily c-terminal 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 2
Similarity search - Component
Biological speciesPeptoclostridium difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsLindic, N. / Loboda, J. / Usenik, A. / Turk, D.
Funding support Slovenia, 1items
OrganizationGrant numberCountry
Slovenian Research AgencyP1-0048 Slovenia
CitationJournal: To Be Published
Title: Crystal structure of the accessory translocation ATPase, SecA2, from Clostridium difficile
Authors: Lindic, N. / Loboda, J. / Usenik, A. / Turk, D.
History
DepositionSep 26, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 7, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein translocase subunit SecA 2


Theoretical massNumber of molelcules
Total (without water)89,6611
Polymers89,6611
Non-polymers00
Water5,675315
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area37570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.99, 96.85, 114.74
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 2


Mass: 89661.172 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Peptoclostridium difficile (strain 630) (bacteria)
Strain: 630 / Gene: secA2, CD630_27920 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q183M9
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 315 / Source method: isolated from a natural source / Formula: H2O

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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: 2.63 Å3/Da / Density % sol: 53.29 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, sitting drop
Details: 0.1M BIS-TRIS propane pH 8.3, 0.2M sodium acetate, 18% w/v PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 42821 / % possible obs: 99.3 % / Redundancy: 7 % / Rrim(I) all: 0.22 / Net I/σ(I): 8.04
Reflection shellResolution: 2.3→2.44 Å / Num. unique obs: 6748 / CC1/2: 0.619 / Rrim(I) all: 1.633

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Processing

Software
NameClassification
MAINrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1tf2

1tf2


Resolution: 2.3→47.55 Å / Cor.coef. Fo:Fc: 0.9221 / Cor.coef. Fo:Fc free: 0.9039 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 28.5
RfactorNum. reflection% reflectionSelection details
Rfree0.2742 42717 100 %NONE
Rwork0.2432 ---
all0.2432 ---
obs0.2432 42717 100 %-
Solvent computationBsol: 13.8 Å2 / ksol: 0.27 e/Å3
Displacement parametersBiso max: 1.35 Å2 / Biso mean: 29.32 Å2 / Biso min: 0.32 Å2
Baniso -1Baniso -2Baniso -3
1-4.222 Å20 Å20 Å2
2---3.731 Å20 Å2
3----0.49 Å2
Refinement stepCycle: LAST / Resolution: 2.3→47.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6174 0 0 315 6489
LS refinement shellResolution: 2.3→2.34 Å
RfactorNum. reflection% reflection
Rfree0.3582 2082 100 %
Rwork0.3341 2082 -
obs--100 %

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