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- PDB-4ys0: Conformational changes of the clamp of the protein translocation ... -

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Basic information

Entry
Database: PDB / ID: 4ys0
TitleConformational changes of the clamp of the protein translocation ATPase SecA from Thermotoga maritima
ComponentsProtein translocase subunit SecA
KeywordsPROTEIN TRANSPORT / Protein translocation / SecA / ATPase
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 / ATP binding / plasma membrane / cytoplasm
Similarity search - Function
SecA P-loop domain / 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 P-loop domain / 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 conserved C-terminal domain / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Protein translocase subunit SecA
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.897 Å
AuthorsChen, Y. / Rapoport, T.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM052586 United States
CitationJournal: J.Mol.Biol. / Year: 2015
Title: Conformational Changes of the Clamp of the Protein Translocation ATPase SecA.
Authors: Chen, Y. / Bauer, B.W. / Rapoport, T.A. / Gumbart, J.C.
History
DepositionMar 16, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 24, 2015Group: Database references
Revision 1.2Jul 20, 2016Group: Data collection
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Derived calculations / Refinement description
Category: pdbx_audit_support / pdbx_struct_oper_list / software
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 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)95,6183
Polymers95,1661
Non-polymers4522
Water8,359464
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.404, 110.160, 115.863
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Protein translocase subunit SecA


Mass: 95166.266 Da / Num. of mol.: 1 / Fragment: UNP residues 2-816
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: secA, TM_1578 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X1R4
#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.: 464 / 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: 2.18 Å3/Da / Density % sol: 43.53 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: imidazole, pH 7.0 methyl-2,4-pentanediol

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97914 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 2, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97914 Å / Relative weight: 1
ReflectionResolution: 1.897→39.92 Å / Num. obs: 65151 / % possible obs: 98.8 % / Redundancy: 3 % / Rsym value: 0.086 / Net I/σ(I): 13.21

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3JUX

3jux


Resolution: 1.897→39.92 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2264 3066 5.07 %
Rwork0.1786 61838 -
obs0.181 65138 98.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 113.63 Å2 / Biso mean: 28.5357 Å2 / Biso min: 7.08 Å2
Refinement stepCycle: final / Resolution: 1.897→39.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6598 0 28 464 7090
Biso mean--18.36 32.23 -
Num. residues----814
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096743
X-RAY DIFFRACTIONf_angle_d1.1119072
X-RAY DIFFRACTIONf_chiral_restr0.047995
X-RAY DIFFRACTIONf_plane_restr0.0051161
X-RAY DIFFRACTIONf_dihedral_angle_d15.5762594
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.897-1.92420.32411270.25762411253894
1.9242-1.9530.29091420.23112550269299
1.953-1.98350.26331260.22212517264399
1.9835-2.0160.26741450.21552582272799
2.016-2.05080.27361560.21532522267899
2.0508-2.08810.27921380.20862544268299
2.0881-2.12820.31881410.20592548268999
2.1282-2.17170.24671270.1982558268599
2.1717-2.21890.28521350.19342572270799
2.2189-2.27050.26251300.18742528265899
2.2705-2.32730.23921420.18242593273599
2.3273-2.39020.23491400.17612579271999
2.3902-2.46050.22231240.17522580270499
2.4605-2.53990.23031430.16942545268899
2.5399-2.63070.25031280.17862592272099
2.6307-2.7360.25181300.179526062736100
2.736-2.86060.2461540.180925772731100
2.8606-3.01130.22671370.178726222759100
3.0113-3.20.21251320.175526292761100
3.2-3.4470.20861280.164626242752100
3.447-3.79380.19091520.15172618277099
3.7938-4.34250.17991360.15272646278299
4.3425-5.470.20791430.1682640278398
5.47-49.76210.19471440.18542655279994

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