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- PDB-1m6n: Crystal structure of the SecA translocation ATPase from Bacillus ... -

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Basic information

Entry
Database: PDB / ID: 1m6n
TitleCrystal structure of the SecA translocation ATPase from Bacillus subtilis
ComponentsPreprotein translocase secA
KeywordsPROTEIN TRANSPORT / protein translocation / atpase / transmembrane transport / helicase family structure / mechanochemisty
Function / homology
Function and homology information


protein-exporting ATPase activity / cell envelope Sec protein transport complex / protein-secreting ATPase / protein transport by the Sec complex / intracellular protein transmembrane transport / protein import / protein targeting / membrane raft / ATP binding / metal ion binding ...protein-exporting ATPase activity / cell envelope Sec protein transport complex / 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 / SEC-C motif / SEC-C motif / Protein translocase subunit SecA / SecA DEAD-like, N-terminal / SecA Wing/Scaffold ...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 / 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, C-terminal helicase domain / SecA preprotein cross-linking domain / SecA Wing and Scaffold domain / SecA DEAD-like domain / SecA P-loop 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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 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 / MIR / Resolution: 2.7 Å
AuthorsHunt, J.F. / Weinkauf, S. / Henry, L. / Fak, J.J. / McNicholas, P. / Oliver, D.B. / Deisenhofer, J.
Citation
Journal: Science / Year: 2002
Title: Nucleotide Control of Interdomain Interactions in the Conformational Reaction Cycle of SecA
Authors: Hunt, J.F. / Weinkauf, S. / Henry, L. / Fak, J.J. / McNicholas, P. / Oliver, D.B. / Deisenhofer, J.
#1: Journal: To be Published / Year: 2002
Title: Ping-pong cross-validation in real space: a method to increase the phasing power of a partial model without risk of phase bias
Authors: Hunt, J.F. / Deisenhofer, J.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Conformational stabilization and crystallization of the SecA translocation ATPase from Bacillus subtilis
Authors: Weinkauf, S. / Hunt, J.F. / Scheuring, J. / Henry, L. / Fak, J.J. / Oliver, D.B. / Deisenhofer, J.
History
DepositionJul 16, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 20, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Preprotein translocase secA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,0668
Polymers91,3941
Non-polymers6727
Water81145
1
A: Preprotein translocase secA
hetero molecules

A: Preprotein translocase secA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)184,13216
Polymers182,7882
Non-polymers1,34514
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-y+1,-x+1,-z+2/31
Buried area8580 Å2
ΔGint-261 kcal/mol
Surface area68480 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)130.833, 130.833, 150.350
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number151
Cell settingtrigonal
Space group name H-MP3112
DetailsThe other subunit in the physiological dimer is generated by 1-y, 1-x, 2/3-z (4_665)

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Components

#1: Protein Preprotein translocase secA / secA


Mass: 91393.758 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: Div / Plasmid: pT7-Div / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P28366
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 4.06 Å3/Da / Density % sol: 69.73 %
Crystal growTemperature: 299 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2 M ammonium sulfate, 30% glycerol, 1 mM DTT, 100 mM BES, pH 7.0, VAPOR DIFFUSION, HANGING DROP at 299K
Crystal grow
*PLUS
Details: Weinkauf, S., (2001) Acta Crystallogr., Sect.D, 57, 559.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
115-20 mg/mlprotein1drop
2300 mMammonium sulfate1drop
31 mMdithiothreitol1drop
420 mMBES1droppH7.0
546-52 %satammonium sulfate1reservoir
628-32 %(v/v)glycerol1reservoir
720-100 mMBES1reservoirpH7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID2 / Wavelength: 0.986 Å
DetectorType: MARRESEARCH / Detector: AREA DETECTOR / Date: Dec 15, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.986 Å / Relative weight: 1
ReflectionResolution: 2.7→45 Å / Num. all: 40576 / Num. obs: 40372 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Biso Wilson estimate: 62 Å2 / Rmerge(I) obs: 0.073 / Rsym value: 0.073 / Net I/σ(I): 18.9
Reflection shellResolution: 2.7→2.75 Å / Mean I/σ(I) obs: 2.14 / Num. unique all: 2018 / % possible all: 0.973
Reflection
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 50 Å / % possible obs: 99.6 % / Rmerge(I) obs: 0.078

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Processing

Software
NameVersionClassification
DMmodel building
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
DMphasing
RefinementMethod to determine structure: MIR / Resolution: 2.7→45.24 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 2936891.3 / 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
Rfree0.301 1616 5 %RANDOM
Rwork0.22 ---
obs0.22 32620 80.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 91.5959 Å2 / ksol: 0.330937 e/Å3
Displacement parametersBiso mean: 98.4 Å2
Baniso -1Baniso -2Baniso -3
1--6.54 Å22.11 Å20 Å2
2---6.54 Å20 Å2
3---13.07 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.53 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.66 Å0.56 Å
Refinement stepCycle: LAST / Resolution: 2.7→45.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6402 0 35 45 6482
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.013
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_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.67
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it7.191.5
X-RAY DIFFRACTIONc_mcangle_it11.262
X-RAY DIFFRACTIONc_scbond_it40.712
X-RAY DIFFRACTIONc_scangle_it39.942.5
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.381 179 5 %
Rwork0.355 3413 -
obs--53.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHTOPH
X-RAY DIFFRACTION2PARTOP
X-RAY DIFFRACTION3PARATOPH
Refinement
*PLUS
Rfactor obs: 0.22 / Rfactor Rfree: 0.304 / Rfactor Rwork: 0.221
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.74
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.67
LS refinement shell
*PLUS
Rfactor Rfree: 0.381 / Rfactor Rwork: 0.355

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