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- PDB-2fsi: Complex SecA:ADP from Escherichia coli -

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Basic information

Entry
Database: PDB / ID: 2fsi
TitleComplex SecA:ADP from Escherichia coli
ComponentsPreprotein translocase secA subunit
KeywordsPROTEIN TRANSPORT / ATPase / DNA-RNA helicase / Protein translocation / SecA
Function / homology
Function and homology information


preprotein binding / protein-exporting ATPase activity / cell envelope Sec protein transport complex / protein-secreting ATPase / intracellular protein transmembrane transport / protein transport by the Sec complex / protein import / protein targeting to membrane / protein secretion / protein targeting ...preprotein binding / protein-exporting ATPase activity / cell envelope Sec protein transport complex / protein-secreting ATPase / intracellular protein transmembrane transport / protein transport by the Sec complex / protein import / protein targeting to membrane / protein secretion / protein targeting / ribonucleoprotein complex binding / : / cytoplasmic side of plasma membrane / protein transport / ribosome binding / zinc ion binding / ATP binding / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Helical scaffold and wing domains of SecA / Helical scaffold and wing domains of SecA / SEC-C motif / SEC-C motif / Protein translocase subunit SecA / SecA DEAD-like, N-terminal / SecA Wing/Scaffold / SecA, preprotein cross-linking domain / SecA motor DEAD / SecA conserved site ...Helical scaffold and wing domains of SecA / Helical scaffold and wing domains of SecA / SEC-C motif / SEC-C motif / 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, C-terminal helicase domain / SecA preprotein cross-linking domain / SecA Wing and Scaffold domain / SecA DEAD-like domain / SecA P-loop 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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 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 speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 Å
AuthorsPapanikolau, Y. / Petratos, K. / Economou, A.
Citation
Journal: J.Mol.Biol. / Year: 2007
Title: Structure of dimeric SecA, the Escherichia coli preprotein translocase motor.
Authors: Papanikolau, Y. / Papadovasilaki, M. / Ravelli, R.B. / McCarthy, A.A. / Cusack, S. / Economou, A. / Petratos, K.
#1: Journal: Febs Lett. / Year: 2005
Title: Escherichia coli SecA truncated at its termini is functional and dimeric
Authors: Karamanou, S. / Sianidis, G. / Gouridis, G. / Pozidis, C. / Papanikolau, Y. / Papanikou, E. / Economou, A.
History
DepositionJan 23, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 16, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
B: Preprotein translocase secA subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)194,9934
Polymers194,1382
Non-polymers8542
Water7,819434
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.560, 90.430, 163.290
Angle α, β, γ (deg.)90.00, 100.82, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Preprotein translocase secA subunit


Mass: 97069.102 Da / Num. of mol.: 2 / Fragment: residues 9-861
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: secA, azi, pea, prlD / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21/pLysS / References: UniProt: P10408
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 434 / 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: 2.82 Å3/Da / Density % sol: 56.41 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9762 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 3, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.11→19.85 Å / Num. all: 124578 / Num. obs: 112860 / % possible obs: 90.6 % / Redundancy: 1.86 % / Biso Wilson estimate: 43.935 Å2 / Rmerge(I) obs: 0.039 / Net I/σ(I): 11.66
Reflection shell
Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.11-2.241.50.223.1152731025651.3
2.24-2.390.174.5323991711691.1
2.39-2.580.116.4321241669095.4
2.58-2.820.0728.8300461563096.5
2.82-3.150.04712.4274241427697.5
3.15-3.630.03317.3240011258797.2
3.63-4.430.02822.6203131073897.6
4.430.02923.216012845198.2

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.2.0005refinement
PDB_EXTRACT1.701data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FSF

2fsf


Resolution: 2.11→19.85 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.913 / SU B: 10.641 / SU ML: 0.146 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.202 / ESU R Free: 0.195 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.263 5666 5 %RANDOM
Rwork0.203 ---
all0.206 124578 --
obs-112860 90.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 39.958 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å2-0.01 Å2
2--0.02 Å20 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 2.11→19.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11448 0 54 434 11936
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.030.02211693
X-RAY DIFFRACTIONr_bond_other_d0.0020.0210768
X-RAY DIFFRACTIONr_angle_refined_deg2.2791.97315786
X-RAY DIFFRACTIONr_angle_other_deg1.09325021
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.23951434
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.99124.152578
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.917152151
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.75915105
X-RAY DIFFRACTIONr_chiral_restr0.1530.21750
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212967
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022320
X-RAY DIFFRACTIONr_nbd_refined0.2380.23056
X-RAY DIFFRACTIONr_nbd_other0.2180.211475
X-RAY DIFFRACTIONr_nbtor_refined0.1890.25563
X-RAY DIFFRACTIONr_nbtor_other0.0970.26984
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1910.2572
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.2130.24
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2170.238
X-RAY DIFFRACTIONr_symmetry_vdw_other0.250.2134
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1830.217
X-RAY DIFFRACTIONr_mcbond_it1.7491.59072
X-RAY DIFFRACTIONr_mcbond_other0.4141.52909
X-RAY DIFFRACTIONr_mcangle_it2.105211522
X-RAY DIFFRACTIONr_scbond_it3.36735148
X-RAY DIFFRACTIONr_scangle_it4.7124.54264
LS refinement shellResolution: 2.11→2.162 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 177 -
Rwork0.263 3136 -
obs-3313 36.48 %

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