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- PDB-5cnx: Crystal structure of Xaa-Pro aminopeptidase from Escherichia coli K12 -
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Open data
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Basic information
Entry | Database: PDB / ID: 5cnx | ||||||
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Title | Crystal structure of Xaa-Pro aminopeptidase from Escherichia coli K12 | ||||||
![]() | Aminopeptidase YpdF | ||||||
![]() | HYDROLASE / Xaa-Pro aminopeptidase / PepQ / prolidase | ||||||
Function / homology | ![]() Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases / metalloaminopeptidase activity / transition metal ion binding / aminopeptidase activity / proteolysis Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kumar, A. / Are, V. / Ghosh, B. / Jamdar, S. / Makde, R.D. | ||||||
![]() | ![]() Title: Structures and activities of widely conserved small prokaryotic aminopeptidases-P clarify classification of M24B peptidases Authors: Are, V.N. / Kumar, A. / Goyal, V.D. / Gotad, S.S. / Ghosh, B. / Gadre, R. / Jamdar, S.N. / Makde, R.D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 422.3 KB | Display | ![]() |
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PDB format | ![]() | 351.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 464.9 KB | Display | ![]() |
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Full document | ![]() | 470.6 KB | Display | |
Data in XML | ![]() | 37 KB | Display | |
Data in CIF | ![]() | 50.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5giqC ![]() 3q6dS 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 3 molecules ABC
#1: Protein | Mass: 39620.641 Da / Num. of mol.: 3 / Mutation: M1S Source method: isolated from a genetically manipulated source Details: genomic DNA / Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P76524, Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases |
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-Non-polymers , 5 types, 61 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/CAC.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CAC.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ZN / #3: Chemical | #4: Chemical | ChemComp-GOL / | #5: Chemical | ChemComp-NA / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.56 Å3/Da / Density % sol: 73 % |
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Crystal grow | Temperature: 293 K / Method: microbatch Details: Crystallization solution: 1.4 M Sodium Citrate, 0.1 M Sodium Cacodylate pH 6.6, 10% glycerol, 1 mM ZnCl2 Protein solution: 20 mM TrisHCl, 200 mM NaCl PH range: 7.2-7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 6, 2014 / Details: mirror |
Radiation | Monochromator: doule crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97947 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→48.9 Å / Num. obs: 66134 / % possible obs: 99.9 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.109 / Net I/σ(I): 10.8 |
Reflection shell | Resolution: 2.6→2.66 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.673 / Mean I/σ(I) obs: 2.1 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3Q6D Resolution: 2.6→48.897 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→48.897 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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