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- PDB-1tf2: Crystal structure of SecA:ADP in an open conformation from Bacill... -

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Basic information

Entry
Database: PDB / ID: 1tf2
TitleCrystal structure of SecA:ADP in an open conformation from Bacillus Subtilis
ComponentsPreprotein translocase secA subunit
KeywordsPROTEIN TRANSPORT / ATPase / helicase / translocation / secretion
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 / membrane raft / ATP binding / metal ion 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 / membrane raft / ATP binding / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
Pre-protein croslinking domain of SecA / SecA, preprotein cross-linking domain / Helical scaffold and wing domains of SecA / Helical scaffold and wing domains of SecA / SecA P-loop domain / SEC-C motif / SEC-C motif / SecA, C-terminal helicase domain / Protein translocase subunit SecA / SecA DEAD-like, N-terminal ...Pre-protein croslinking domain of SecA / SecA, preprotein cross-linking domain / Helical scaffold and wing domains of SecA / Helical scaffold and wing domains of SecA / 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 nucleotide triphosphate hydrolases / Alpha-Beta Complex / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Protein translocase subunit SecA
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsOsborne, A.R. / Clemons Jr., W.M. / Rapoport, T.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2004
Title: A large conformational change of the translocation ATPase SecA.
Authors: Osborne, A.R. / Clemons Jr., W.M. / Rapoport, T.A.
History
DepositionMay 26, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_label_seq_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_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Preprotein translocase secA subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,4083
Polymers95,9561
Non-polymers4522
Water46826
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)149.232, 107.189, 72.054
Angle α, β, γ (deg.)90.00, 94.96, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Preprotein translocase secA subunit


Mass: 95956.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: SECA, DIV+, BSU35300 / Plasmid: modified pet19b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-RIL / References: UniProt: P28366
#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.: 26 / 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: 2.99 Å3/Da / Density % sol: 58.88 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1M HEPES, 250mM Magnesium Acetate, 7-12% PEG 8000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.97903 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97903 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 25014 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 44.4 Å2 / Rsym value: 0.073
Reflection shellResolution: 2.9→3 Å / Rsym value: 0.479 / % possible all: 94

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB enrty 1M6N

1m6n


Resolution: 2.9→44.98 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 210220.53 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.292 2595 5.6 %RANDOM
Rwork0.228 ---
obs0.228 25014 93.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 12.541 Å2 / ksol: 0.276135 e/Å3
Displacement parametersBiso mean: 61.5 Å2
Baniso -1Baniso -2Baniso -3
1--14.99 Å20 Å22.66 Å2
2--5.43 Å20 Å2
3---9.56 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.49 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.58 Å0.57 Å
Refinement stepCycle: LAST / Resolution: 2.9→44.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6163 0 28 26 6217
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d21
X-RAY DIFFRACTIONc_improper_angle_d0.72
LS refinement shellResolution: 2.9→3 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.452 221 6 %
Rwork0.386 3460 -
obs--75.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMWATER.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMION.TOP
X-RAY DIFFRACTION40519_ADP_PAR.TXT0519_ADP_TOP.TXT

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