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- PDB-3jux: Structure of the translocation ATPase SecA from Thermotoga maritima -

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Basic information

Entry
Database: PDB / ID: 3jux
TitleStructure of the translocation ATPase SecA from Thermotoga maritima
ComponentsProtein translocase subunit secA
KeywordsPROTEIN TRANSPORT / protein translocation / ATPase / conformational change / peptide binding / ATP-binding / Cell inner membrane / Cell membrane / Cytoplasm / Membrane / Nucleotide-binding / Translocation / Transport
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 import / protein targeting / ATP binding / plasma membrane / cytoplasm
Similarity search - Function
SecA P-loop 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 P-loop 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 conserved C-terminal domain / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Protein translocase subunit SecA
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsZimmer, J.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Conformational flexibility and peptide interaction of the translocation ATPase SecA.
Authors: Zimmer, J. / Rapoport, T.A.
History
DepositionSep 15, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650HELIX DETERMINATION METHOD: AUTHOR
Remark 700SHEET DETERMINATION METHOD: AUTHOR

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein translocase subunit secA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,3753
Polymers94,9241
Non-polymers4522
Water362
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.533, 119.403, 120.820
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailsmonomer

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Components

#1: Protein Protein translocase subunit secA


Mass: 94923.992 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: DSM 3109 / Gene: secA, TM_1578 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): C43 / References: UniProt: Q9X1R4
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 49.83 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M Hepes pH 7.5, 60% MPD, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.29 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 29, 2008
Details: double crystal monochromater with horizontal focusing sagittal bend second mono crystal with 4:1 magnification ratio and vertically focusing mirror.
RadiationMonochromator: double crystal monochromater / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.29 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. all: 19431 / Num. obs: 17570 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 6.8 % / Rsym value: 0.173 / Net I/σ(I): 13.6
Reflection shellResolution: 3.1→3.22 Å / Redundancy: 6.7 % / Mean I/σ(I) obs: 2.5 / Num. unique all: 1913 / Rsym value: 0.79 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TF5

1tf5


Resolution: 3.1→30 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 1.5 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.303 1560 -RANDOM
Rwork0.227 ---
all-15597 --
obs-17570 100 %-
Displacement parametersBiso mean: 42.3 Å2
Refinement stepCycle: LAST / Resolution: 3.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6589 0 28 2 6619
LS refinement shellResolution: 3.1→3.13 Å /
RfactorNum. reflection
Rfree0.527 46
Rwork0.387 -
obs-384

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