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- PDB-5k9t: SecA-N68, a C-terminal truncation of the SecA ATPase from E. coli -

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Basic information

Entry
Database: PDB / ID: 5k9t
TitleSecA-N68, a C-terminal truncation of the SecA ATPase from E. coli
ComponentsProtein translocase subunit SecA
KeywordsPROTEIN TRANSPORT / preprotein translocase / SecA-N68 / ATPase / C-terminal truncation / N-terminus / peptide binding
Function / homology
Function and homology information


protein-secreting ATPase / intracellular protein transmembrane transport / protein import / protein targeting / ATP binding / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
Pre-protein croslinking domain of SecA / SecA, preprotein cross-linking domain / 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 ...Pre-protein croslinking domain of SecA / SecA, preprotein cross-linking domain / 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 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 / 3-Layer(aba) Sandwich / 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: 2.6 Å
AuthorsShilton, B.H. / Vezina, G.C.
CitationJournal: Sci Rep / Year: 2017
Title: An alternate mode of oligomerization for E. coli SecA.
Authors: Yazdi, A.K. / Vezina, G.C. / Shilton, B.H.
History
DepositionJun 1, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 7, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Sep 27, 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
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein translocase subunit SecA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,7383
Polymers64,2871
Non-polymers4522
Water2,162120
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area890 Å2
ΔGint-19 kcal/mol
Surface area28470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.065, 64.450, 87.967
Angle α, β, γ (deg.)90.000, 105.850, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Protein translocase subunit SecA


Mass: 64286.848 Da / Num. of mol.: 1
Mutation: entropy-reducing mutations E55A, K56A, E58A, E196A, and E197A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain 55989 / EAEC) (bacteria)
Strain: 55989 / EAEC / Gene: secA, EC55989_0094 / Production host: Escherichia coli (E. coli) / References: UniProt: B7LFW8
#2: 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
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 2.85 Å3/Da / Density % sol: 56.89 % / Description: plates
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1M Tris-HCl pH 8.0, 18% PEG 3000, and 0.9% w/v cadaverine; 18 mg/mL protein concentration. Cryoprotectant included 18% PEG 3000 and 20% PEG 200

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1.105535 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 15, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.105535 Å / Relative weight: 1
ReflectionResolution: 2.59→84.623 Å / Num. obs: 22456 / % possible obs: 99.4 % / Redundancy: 4 % / Biso Wilson estimate: 35.03 Å2 / Rsym value: 0.12 / Net I/av σ(I): 5.858 / Net I/σ(I): 8.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.59-2.7340.5111.5196.8
2.73-2.940.382199.9
2.9-3.14.10.2692.91100
3.1-3.354.10.1744.41100
3.35-3.674.10.1265.91100
3.67-4.14.10.1116.31100
4.1-4.734.10.0729.11100
4.73-5.84.10.06510.4199.8
5.8-8.240.04614.7199.6
8.2-40.8683.90.02820197.8

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
SCALA3.3.21data scaling
PDB_EXTRACT3.2data extraction
iMOSFLMdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BXZ and 5K94

3bxz

5k94


Resolution: 2.6→17.916 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2497 2216 9.93 %
Rwork0.1956 20100 -
obs0.2009 22316 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 125.23 Å2 / Biso mean: 47.7153 Å2 / Biso min: 7.55 Å2
Refinement stepCycle: final / Resolution: 2.6→17.916 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4503 0 40 120 4663
Biso mean--27.11 29.2 -
Num. residues----576
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064609
X-RAY DIFFRACTIONf_angle_d0.7696225
X-RAY DIFFRACTIONf_chiral_restr0.044702
X-RAY DIFFRACTIONf_plane_restr0.004816
X-RAY DIFFRACTIONf_dihedral_angle_d14.0282805
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6001-2.65640.34561270.24751233136099
2.6564-2.7180.35621380.24212461384100
2.718-2.78570.28511410.227112521393100
2.7857-2.86080.29841330.223712361369100
2.8608-2.94460.24971450.217912731418100
2.9446-3.03920.29271360.218412461382100
3.0392-3.14730.28171370.231312331370100
3.1473-3.27250.28031390.228912631402100
3.2725-3.42050.32351400.228112441384100
3.4205-3.59950.27081400.215212551395100
3.5995-3.82290.22961350.199512721407100
3.8229-4.11480.22721370.185412561393100
4.1148-4.52290.20831420.160512701412100
4.5229-5.16360.19771410.152112741415100
5.1636-6.45460.22631400.189412561396100
6.4546-17.91610.19471450.14961291143699
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.2358-0.16990.03151.3177-0.49760.64360.0013-0.04610.0925-0.00660.0277-0.0077-0.07140.0014-0.03270.14510.00310.00580.1513-0.05780.149911.033614.48696.0752
2-0.1131-0.0384-0.22160.3324-1.36630.82740.0026-0.0254-0.0864-0.15260.01940.07350.4315-0.04790.02790.8575-0.12640.03910.40120.02440.38157.1929-29.757634.8081
31.2491-0.50330.64130.7672-0.39831.0562-0.1728-0.29780.1680.18310.1434-0.2163-0.02980.0306-0.0030.19360.0534-0.0050.293-0.10920.253935.842711.320717.44
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 15 through 215 )A15 - 215
2X-RAY DIFFRACTION2chain 'A' and (resid 216 through 383 )A216 - 383
3X-RAY DIFFRACTION3chain 'A' and (resid 384 through 590 )A384 - 590

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