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- PDB-3b2p: Crystal structure of E. coli Aminopeptidase N in complex with arginine -
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Open data
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Basic information
Entry | Database: PDB / ID: 3b2p | ||||||
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Title | Crystal structure of E. coli Aminopeptidase N in complex with arginine | ||||||
![]() | Aminopeptidase N | ||||||
![]() | HYDROLASE / Protease / aminopeptidase N / thermolysin / Membrane / Metal-binding / Metalloprotease / ---- | ||||||
Function / homology | ![]() membrane alanyl aminopeptidase / aminopeptidase activity / metallopeptidase activity / proteolysis / zinc ion binding / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Anthony, A. / Leslie, G. / Matthews, B.W. | ||||||
![]() | ![]() Title: Structural basis for the unusual specificity of Escherichia coli aminopeptidase N. Authors: Addlagatta, A. / Gay, L. / Matthews, B.W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 213 KB | Display | ![]() |
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PDB format | ![]() | 166.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 475.5 KB | Display | ![]() |
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Full document | ![]() | 484.9 KB | Display | |
Data in XML | ![]() | 40.4 KB | Display | |
Data in CIF | ![]() | 62.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3b2xC ![]() 3b34C ![]() 3b37C ![]() 3b3bC ![]() 2hpoS 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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1 |
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 101441.195 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 6 types, 781 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/ARG.gif)
![](data/chem/img/MLI.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/ARG.gif)
![](data/chem/img/MLI.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ZN / | ||||||||
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#3: Chemical | #4: Chemical | ChemComp-ARG / | #5: Chemical | ChemComp-MLI / | #6: Chemical | ChemComp-GOL / #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.49 Å3/Da / Density % sol: 64.74 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 1.8 M Sodium malonate pH=7/0, pH 7.00, 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: Jan 25, 2007 / Details: KOHZU: Double Crystal Si(111) |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. all: 95605 / Num. obs: 95605 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.6 % / Biso Wilson estimate: 22.885 Å2 / Rmerge(I) obs: 0.1 / Rsym value: 0.08 / Net I/σ(I): 13.2 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 5 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 2.4 / Num. unique all: 9360 / Rsym value: 0.5 / % possible all: 99.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2HPO Resolution: 2→44.37 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.946 / SU B: 3.001 / SU ML: 0.082 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 20 / ESU R: 0.114 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.646 Å2
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Refinement step | Cycle: LAST / Resolution: 2→44.37 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.002→2.054 Å / Total num. of bins used: 20
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