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- PDB-3n33: Crystal structure of the N-terminal beta-aminopeptidase BapA in c... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3n33 | ||||||
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Title | Crystal structure of the N-terminal beta-aminopeptidase BapA in complex with pefabloc SC (AEBSF) | ||||||
![]() | Beta-peptidyl aminopeptidase | ||||||
![]() | Hydrolase/Hydrolase Inhibitor / Ntn hydrolase / alpha-beta-beta-alpha sandwich / beta-aminopeptidase / Hydrolase-Hydrolase Inhibitor complex | ||||||
Function / homology | ![]() beta-peptidyl aminopeptidase / aminopeptidase activity / periplasmic space / proteolysis / identical protein binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Merz, T. / Heck, T. / Geueke, B. / Kohler, H.-P. / Gruetter, M.G. | ||||||
![]() | ![]() Title: Autoproteolytic and catalytic mechanisms for the beta-aminopeptidase BapA--a member of the Ntn hydrolase family. Authors: Merz, T. / Heck, T. / Geueke, B. / Mittl, P.R. / Briand, C. / Seebach, D. / Kohler, H.P. / Grutter, M.G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 307.3 KB | Display | ![]() |
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PDB format | ![]() | 247.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 505.4 KB | Display | ![]() |
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Full document | ![]() | 521.7 KB | Display | |
Data in XML | ![]() | 66.4 KB | Display | |
Data in CIF | ![]() | 96.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3n2wSC ![]() 3n5iC 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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Unit cell |
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Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 38634.836 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: bapA / Plasmid: pYBapA / Production host: ![]() ![]() |
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-Non-polymers , 5 types, 1295 molecules 








#2: Chemical | ChemComp-GOL / #3: Chemical | #4: Chemical | ChemComp-AES / #5: Chemical | ChemComp-SO4 / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.63 Å3/Da / Density % sol: 53.28 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 1.5M ammonium sulfate, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 16, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→48.425 Å / Num. all: 148269 / Num. obs: 144719 / % possible obs: 97.6 % / Observed criterion σ(I): 3 / Redundancy: 3.78 % / Rmerge(I) obs: 0.135 / Rsym value: 0.01 / Net I/σ(I): 12.87 |
Reflection shell | Resolution: 1.8→1.85 Å / Redundancy: 3.69 % / Rmerge(I) obs: 0.578 / Mean I/σ(I) obs: 3.07 / Num. unique all: 11042 / Rsym value: 0.497 / % possible all: 94.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 3N2W Resolution: 1.8→48.067 Å / SU ML: 0.19 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / 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: 44.929 Å2 / ksol: 0.375 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.56 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→48.067 Å
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Refine LS restraints |
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LS refinement shell |
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