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Open data
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Basic information
Entry | Database: PDB / ID: 3jv2 | ||||||
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Title | Crystal Structure of B. subtilis SecA with bound peptide | ||||||
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![]() | PROTEIN TRANSPORT / protein translocation / ATPase / conformational change / peptide binding / ATP-binding / Cell membrane / Cytoplasm / Membrane / Metal-binding / Nucleotide-binding / Translocation / Transport / Zinc | ||||||
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 / helicase activity / membrane raft / ATP 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 / helicase activity / membrane raft / ATP binding / metal ion binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zimmer, J. | ||||||
![]() | ![]() Title: Conformational flexibility and peptide interaction of the translocation ATPase SecA. Authors: Zimmer, J. / Rapoport, T.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 621.8 KB | Display | ![]() |
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PDB format | ![]() | 515.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 60.4 KB | Display | |
Data in CIF | ![]() | 82.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3juxC ![]() 1tf5S 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 89208.500 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein/peptide | Mass: 273.330 Da / Num. of mol.: 2 / Source method: obtained synthetically #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Sequence details | THE SEQUENCE OF THE PEPTIDE IS IRKYGGYIPGLRPGRSTEQYLHR. AUTHORS STATE THAT THE SEQUENCE CANNOT ...THE SEQUENCE OF THE PEPTIDE IS IRKYGGYIPG | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.79 Å3/Da / Density % sol: 55.98 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 0.1M sodium citrate, 8% PEG 4000, 0.1M NaCl, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 11, 2007 Details: Rosenbaum-Rock high-resolution double-crystal monochromator |
Radiation | Monochromator: Rosenbaum-Rock high-resolution double-crystal monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 67929 / % possible obs: 98.3 % / Observed criterion σ(F): 1.5 / Observed criterion σ(I): 2 / Redundancy: 5.4 % / Rsym value: 0.069 / Net I/σ(I): 26.4 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 2.8 / Num. unique all: 6644 / Rsym value: 0.46 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: pdb entry 1TF5 Resolution: 2.5→30 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 19.7 Å2 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→30 Å
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LS refinement shell | Resolution: 2.5→2.52 Å /
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