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- PDB-4xmx: Crystal Structure of Met260Ala mutant of E. coli Aminopeptidase N... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4xmx | ||||||
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Title | Crystal Structure of Met260Ala mutant of E. coli Aminopeptidase N in complex with Bestatin | ||||||
![]() | Aminopeptidase N | ||||||
![]() | HYDROLASE | ||||||
Function / homology | ![]() membrane alanyl aminopeptidase / aminopeptidase activity / metallopeptidase activity / proteolysis / zinc ion binding / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Addlagatta, A. / Gumpena, R. / Kishor, C. | ||||||
![]() | ![]() Title: Crystal Structure of Met260Ala mutant of E. coli Aminopeptidase N in complex with Bestatin Authors: Addlagatta, A. / Gumpena, R. / Kishor, C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 210 KB | Display | ![]() |
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PDB format | ![]() | 161.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 809.6 KB | Display | ![]() |
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Full document | ![]() | 820.3 KB | Display | |
Data in XML | ![]() | 39.2 KB | Display | |
Data in CIF | ![]() | 59.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2hpoS ![]() 4xms 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 98479.961 Da / Num. of mol.: 1 / Fragment: UNP residues 5-870 / Mutation: M260A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: K12 / Gene: pepN, b0932, JW0915 / Plasmid: pET15b / Production host: ![]() ![]() |
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-Non-polymers , 6 types, 682 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/BES.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/MLI.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/BES.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/MLI.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ZN / | ||||||
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#3: Chemical | ChemComp-BES / | ||||||
#4: Chemical | ChemComp-NA / #5: Chemical | ChemComp-GOL / #6: Chemical | ChemComp-MLI / #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.64 Å3/Da / Density % sol: 66.25 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: Sodium malonate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 21, 2014 |
Radiation | Monochromator: Cu / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→20.81 Å / Num. obs: 64564 / % possible obs: 99.9 % / Redundancy: 5.5 % / Rsym value: 0.16 / Net I/σ(I): 9.94 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 5.4 % / Mean I/σ(I) obs: 3.02 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2HPO Resolution: 2.3→20.81 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.941 / SU B: 4.786 / SU ML: 0.114 / Cross valid method: THROUGHOUT / ESU R: 0.173 / ESU R Free: 0.16 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 25.708 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→20.81 Å
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Refine LS restraints |
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