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- PDB-3slj: Pre-cleavage Structure of the Autotransporter EspP - N1023A mutant -
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Open data
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Basic information
Entry | Database: PDB / ID: 3slj | ||||||
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Title | Pre-cleavage Structure of the Autotransporter EspP - N1023A mutant | ||||||
![]() | Serine protease espP | ||||||
![]() | PROTEIN TRANSPORT / beta barrel / membrane protein / asparagine cyclization / autocleavage | ||||||
Function / homology | ![]() Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / cell outer membrane / periplasmic space / serine-type endopeptidase activity / cell surface / proteolysis / extracellular region Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Barnard, T.B. / Noinaj, N. / Easley, N.C. / Kuszak, A.J. / Buchanan, S.K. | ||||||
![]() | ![]() Title: Molecular basis for the activation of a catalytic asparagine residue in a self-cleaving bacterial autotransporter. Authors: Barnard, T.J. / Gumbart, J. / Peterson, J.H. / Noinaj, N. / Easley, N.C. / Dautin, N. / Kuszak, A.J. / Tajkhorshid, E. / Bernstein, H.D. / Buchanan, S.K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 135.5 KB | Display | ![]() |
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PDB format | ![]() | 104.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 15.1 KB | Display | |
Data in CIF | ![]() | 19.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3sloC ![]() 3sltC ![]() 2qomS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 34417.996 Da / Num. of mol.: 1 Fragment: Autotransporter protein espP translocator (UNP residues 999-1300) Mutation: N1023A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||
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#2: Chemical | ChemComp-C8E / ( #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.41 Å3/Da / Density % sol: 63.96 % |
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Crystal grow | Temperature: 294 K / pH: 7.5 Details: 20% w/v PEG8000, 20% v/v glycerol, pH 7.5, HANGING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 18, 2009 / Details: mirrors | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si 220 (ROSENBAUM-ROCK DOUBLE-CRYSTAL MONOCHROMATOR) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.48→50 Å / Num. all: 17548 / Num. obs: 17443 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Rmerge(I) obs: 0.087 / Χ2: 1.04 / Net I/σ(I): 9.5 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR | Rfactor: 50.9 / Model details: Phaser MODE: MR_AUTO
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2QOM Resolution: 2.481→43.426 Å / Occupancy max: 1 / Occupancy min: 0.41 / FOM work R set: 0.8267 / SU ML: 0.35 / σ(F): 1.34 / Phase error: 23.13 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 63.558 Å2 / ksol: 0.36 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 99.98 Å2 / Biso mean: 46.1032 Å2 / Biso min: 18.96 Å2
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Refinement step | Cycle: LAST / Resolution: 2.481→43.426 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6
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Refinement TLS params. | S33: 0 Å ° / Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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