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- PDB-2ipc: Crystal structure of the translocation ATPase SecA from Thermus t... -

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Basic information

Entry
Database: PDB / ID: 2ipc
TitleCrystal structure of the translocation ATPase SecA from Thermus thermophilus reveals a parallel, head-to-head dimer
ComponentsPreprotein translocase SecA subunit
KeywordsTRANSPORT PROTEIN / nucleotide binding fold / ATPase / parallel dimer / Structural Genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


intracellular protein transmembrane transport / protein import / protein targeting / ATP 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 / Protein translocase subunit SecA / SecA DEAD-like, N-terminal / SecA Wing/Scaffold / SecA, preprotein cross-linking domain / SecA motor DEAD / SecA conserved site ...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 / 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 / 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
Protein translocase subunit SecA
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.8 Å
AuthorsVassylyev, D.G. / Mori, H. / Vassylyeva, M.N. / Tsukazaki, T. / Kimura, Y. / Tahirov, T.H. / Ito, K. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Crystal Structure of the Translocation ATPase SecA from Thermus thermophilus Reveals a Parallel, Head-to-Head Dimer.
Authors: Vassylyev, D.G. / Mori, H. / Vassylyeva, M.N. / Tsukazaki, T. / Kimura, Y. / Tahirov, T.H. / Ito, K.
History
DepositionOct 12, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 28, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Preprotein translocase SecA subunit
B: Preprotein translocase SecA subunit
C: Preprotein translocase SecA subunit
D: Preprotein translocase SecA subunit


Theoretical massNumber of molelcules
Total (without water)456,5294
Polymers456,5294
Non-polymers00
Water24,6811370
1
A: Preprotein translocase SecA subunit
B: Preprotein translocase SecA subunit


Theoretical massNumber of molelcules
Total (without water)228,2642
Polymers228,2642
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Preprotein translocase SecA subunit
D: Preprotein translocase SecA subunit


Theoretical massNumber of molelcules
Total (without water)228,2642
Polymers228,2642
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)168.623, 168.623, 149.758
Angle α, β, γ (deg.)90, 90, 120
Int Tables number145
Space group name H-MP32

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Components

#1: Protein
Preprotein translocase SecA subunit


Mass: 114132.219 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: SecA / Plasmid: pHM451 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5SIW3
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1370 / 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: 2.69 Å3/Da / Density % sol: 54.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 9% PEG4000, 60mM lithium sulfate, 0.2M NaCl, 87.5 mM Tris-HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Mar 15, 2002
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→40 Å / Num. all: 117271 / Num. obs: 114222 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Rmerge(I) obs: 0.058 / Rsym value: 0.058 / Net I/σ(I): 17.9
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.409 / Mean I/σ(I) obs: 4.2 / Num. unique all: 10542 / Rsym value: 0.409 / % possible all: 92.3

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Processing

Software
NameVersionClassification
CrystalClear(MSC/RIGAKU)data collection
MLPHAREphasing
CNS1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MIR / Resolution: 2.8→40 Å / Isotropic thermal model: isotropic / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: The perfect merohedral twinning (twinning fraction = 0.5) was detected with twinning operator {+h,-h-k,-l}. The refinement was carried out against twinned data using the twinning option of the CNS program.
RfactorNum. reflection% reflectionSelection details
Rfree0.2545 6730 -random
Rwork0.2213 ---
all0.2213 117271 --
obs0.2213 114222 97.4 %-
Displacement parametersBiso mean: 59.1 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.62 Å0.54 Å
Refinement stepCycle: LAST / Resolution: 2.8→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30132 0 0 1370 31502
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_angle_deg1.86
LS refinement shellResolution: 2.8→2.9 Å
RfactorNum. reflection% reflection
Rfree0.3033 599 -
Rwork0.2889 --
obs-10139 92.3 %

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