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- PDB-3iqy: Active site mutants of B. subtilis SecA -

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Basic information

Entry
Database: PDB / ID: 3iqy
TitleActive site mutants of B. subtilis SecA
ComponentsProtein translocase subunit secA
KeywordsPROTEIN TRANSPORT / alpha beta / ATP-binding / Cell membrane / Membrane / Metal-binding / Nucleotide-binding / Translocation / Transport
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 / membrane raft / ATP binding / metal ion 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 / membrane raft / ATP binding / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A - #230 / 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 / SecA P-loop domain / SEC-C motif / SEC-C motif / SecA, C-terminal helicase domain / Protein translocase subunit SecA ...Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A - #230 / 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 / 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 / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding 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 speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsKim, D. / Hunt, J.F.
CitationJournal: J.Am.Chem.Soc. / Year: 2013
Title: ATPase Active-Site Electrostatic Interactions Control the Global Conformation of the 100 kDa SecA Translocase.
Authors: Kim, D.M. / Zheng, H. / Huang, Y.J. / Montelione, G.T. / Hunt, J.F.
History
DepositionAug 21, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 11, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 6, 2013Group: Database references
Revision 1.3Apr 3, 2013Group: Database references
Revision 1.4Oct 13, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein translocase subunit secA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,0195
Polymers95,6351
Non-polymers3844
Water0
1
A: Protein translocase subunit secA
hetero molecules

A: Protein translocase subunit secA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)192,03810
Polymers191,2702
Non-polymers7698
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_556x,x-y,-z+11
Buried area5240 Å2
ΔGint-16.4 kcal/mol
Surface area72280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.015, 131.015, 151.966
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number151
Space group name H-MP3112
DetailsAUTHORS STATE THAT THE ASSEMBLY OF THE BIOLOGICAL UNIT THAT IS SHOWN IN REMARK 350 IS PUTATIVE AT THE TIME OF DEPOSITION.

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Components

#1: Protein Protein translocase subunit secA


Mass: 95634.781 Da / Num. of mol.: 1 / Mutation: E208Q, R489K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: BSU35300, div, div+, secA / Plasmid: pT7-Div / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P28366
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4

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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: 3.94 Å3/Da / Density % sol: 68.76 %
Crystal growTemperature: 299 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20 mM BES pH 7.0, 2.1 M Ammonium sulfate, 32 % Glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 299K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 20, 2006 / Details: mirrors
RadiationMonochromator: Si(111) channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.3→30 Å / Num. all: 22533 / Num. obs: 22533 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.9 % / Biso Wilson estimate: 84 Å2 / Rmerge(I) obs: 0.091 / Rsym value: 0.061 / Net I/σ(I): 22.8
Reflection shellResolution: 3.3→3.42 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.683 / Mean I/σ(I) obs: 2.9 / Num. unique all: 2216 / Rsym value: 0.727 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
CNS1.2refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1M6N

1m6n


Resolution: 3.3→19.77 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 370437.21 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.269 912 4.8 %RANDOM
Rwork0.207 ---
all0.22 19062 --
obs0.207 19062 84.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 72.4289 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 101.4 Å2
Baniso -1Baniso -2Baniso -3
1--9.35 Å20 Å20 Å2
2---9.35 Å20 Å2
3---18.69 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.35 Å0.37 Å
Refinement stepCycle: LAST / Resolution: 3.3→19.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6399 0 20 0 6419
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.81
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 3.3→3.42 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.265 64 4.9 %
Rwork0.248 1251 -
obs-2216 59.2 %

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