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Open data
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Basic information
Entry | Database: PDB / ID: 1m74 | ||||||
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Title | Crystal structure of Mg-ADP-bound SecA from Bacillus subtilis | ||||||
![]() | Preprotein translocase secA | ||||||
![]() | PROTEIN TRANSPORT / protein translocation / atpase / transmembrane transport / helicase family structure / mechanochemisty | ||||||
Function / homology | ![]() 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 / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hunt, J.F. / Weinkauf, S. / Henry, L. / Fak, J.J. / McNicholas, P. / Oliver, D.B. / Deisenhofer, J. | ||||||
![]() | ![]() 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: ![]() 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: ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 175.8 KB | Display | ![]() |
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PDB format | ![]() | 138.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 772.5 KB | Display | ![]() |
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Full document | ![]() | 814.1 KB | Display | |
Data in XML | ![]() | 34.9 KB | Display | |
Data in CIF | ![]() | 47.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1m6nSC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Details | The second part of the biological assembly is generated by the two fold axis: 1-y, 1-x, 2/3-z |
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Components
#1: Protein | Mass: 91393.758 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||
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#2: Chemical | ChemComp-MG / | ||||
#3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-ADP / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.09 Å3/Da / Density % sol: 69.94 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 299 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 5 mM ADP, 5 mM MgCl, 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
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: AREA DETECTOR / Date: Dec 15, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.986 Å / Relative weight: 1 |
Reflection | Resolution: 3→50 Å / Num. all: 29711 / Num. obs: 29652 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Biso Wilson estimate: 58.3 Å2 / Rmerge(I) obs: 0.074 / Rsym value: 0.074 / Net I/σ(I): 20.6 |
Reflection shell | Resolution: 3→3.05 Å / Mean I/σ(I) obs: 1.38 / Num. unique all: 1484 / % possible all: 99.8 |
Reflection | *PLUS Highest resolution: 3 Å / Rmerge(I) obs: 0.074 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1M6N Resolution: 3→49.45 Å / Rfactor Rfree error: 0.009 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 90.8636 Å2 / ksol: 0.317385 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 106.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3→49.45 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.19 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 3 Å / Lowest resolution: 50 Å / Rfactor obs: 0.217 / Rfactor Rfree: 0.294 / Rfactor Rwork: 0.218 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.356 / Rfactor Rwork: 0.306 |