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- PDB-2fsg: Complex SecA:ATP from Escherichia coli -

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Basic information

Entry
Database: PDB / ID: 2fsg
TitleComplex SecA:ATP from Escherichia coli
ComponentsPreprotein translocase secA subunit
KeywordsPROTEIN TRANSPORT / ATPase / DNA-RNA helicase / Protein translocation / SecA
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
Protein translocase subunit SecA, preprotein binding 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 ...Protein translocase subunit SecA, preprotein binding 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 / cAMP-dependent Protein Kinase, Chain A / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleotide triphosphate hydrolases / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Protein translocase subunit SecA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)198,1544
Polymers197,1402
Non-polymers1,0142
Water7,764431
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.382, 89.478, 163.349
Angle α, β, γ (deg.)90.00, 100.73, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Preprotein translocase secA subunit


Mass: 98569.797 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-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 431 / 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: 2.74 Å3/Da / Density % sol: 55.19 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.97889 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97889 Å / Relative weight: 1
ReflectionRedundancy: 3.5 % / Av σ(I) over netI: 8.5 / Number: 371706 / Rmerge(I) obs: 0.077 / Rsym value: 0.077 / D res high: 2.2 Å / D res low: 160.491 Å / Num. obs: 105141 / % possible obs: 96.9
Diffraction reflection shell

ID: 1

Highest resolution (Å)Lowest resolution (Å)Num. obs% possible obs (%)Rmerge(I) obsRsym valueRedundancy
6.9659.74353999.50.020.023.7
4.926.9663681000.0440.0443.8
4.024.9281661000.0410.0413.9
3.484.0296311000.0480.0483.8
3.113.48109131000.0660.0663.6
2.843.111192798.90.1170.1173.4
2.632.841272497.50.1980.1983.4
2.462.631341195.50.3080.3083.4
2.322.461400493.70.450.453.4
2.22.3214458920.6440.6443.4
ReflectionResolution: 2.2→20 Å / Num. all: 110188 / Num. obs: 106818 / % possible obs: 96.9 % / Redundancy: 3.5 % / Biso Wilson estimate: 36.38 Å2 / Rmerge(I) obs: 0.077 / Rsym value: 0.077 / Net I/σ(I): 8.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRsym value% possible all
2.2-2.323.40.6441.149535144580.64492
2.32-2.463.40.451.647643140040.4593.7
2.46-2.633.40.3082.445273134110.30895.5
2.63-2.843.40.1983.843017127240.19897.5
2.84-3.113.40.1176.341112119270.11798.9
3.11-3.483.60.06610.939424109130.066100
3.48-4.023.80.04813.13670796310.048100
4.02-4.923.90.04114.53153081660.041100
4.92-6.963.80.04413.22442363680.044100
6.96-59.743.70.0229.71304235390.0299.5

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
REFMAC5.2.0005refinement
PDB_EXTRACT1.701data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
SHELXDphasing
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→19.61 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.899 / SU B: 12.548 / SU ML: 0.165 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.223 / ESU R Free: 0.21 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27 5245 5 %RANDOM
Rwork0.208 ---
all0.211 ---
obs-104943 96.94 %-
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: 17.965 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.2→19.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11316 0 62 431 11809
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0340.02211569
X-RAY DIFFRACTIONr_bond_other_d0.0020.0210676
X-RAY DIFFRACTIONr_angle_refined_deg2.41.97415623
X-RAY DIFFRACTIONr_angle_other_deg1.417324799
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.42251417
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.41424.064566
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.921152128
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.55515104
X-RAY DIFFRACTIONr_chiral_restr0.1430.21734
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212799
X-RAY DIFFRACTIONr_gen_planes_other0.0040.022299
X-RAY DIFFRACTIONr_nbd_refined0.2430.23042
X-RAY DIFFRACTIONr_nbd_other0.2290.211326
X-RAY DIFFRACTIONr_nbtor_refined0.1920.25481
X-RAY DIFFRACTIONr_nbtor_other0.0970.26896
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1870.2559
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1220.25
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1830.249
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2430.2176
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2050.210
X-RAY DIFFRACTIONr_mcbond_it1.971.58358
X-RAY DIFFRACTIONr_mcbond_other0.2771.52874
X-RAY DIFFRACTIONr_mcangle_it2.181211391
X-RAY DIFFRACTIONr_scbond_it3.73735034
X-RAY DIFFRACTIONr_scangle_it5.2124.54232
LS refinement shellResolution: 2.2→2.256 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 353 -
Rwork0.252 6852 -
obs-7205 91.55 %

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