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- PDB-4oid: Structural and kinetic bases for the metal preference of the M18 ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4oid | ||||||
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Title | Structural and kinetic bases for the metal preference of the M18 aminopeptidase from Pseudomonas aeruginosa | ||||||
![]() | Probable M18 family aminopeptidase 2 | ||||||
![]() | HYDROLASE / Dodecameric TET structure / Aspartyl aminopeptidase / Pseudomonas aeruginosa / Aspartic mutation / M18 family | ||||||
Function / homology | ![]() Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases / metalloaminopeptidase activity / proteolysis / zinc ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Nguyen, D.D. / Pandian, R. / Kim, D.D. / Ha, S.C. / Yoon, H.J. / Kim, K.S. / Yun, K.H. / Kim, J.H. / Kim, K.K. | ||||||
![]() | ![]() Title: Structural and kinetic bases for the metal preference of the M18 aminopeptidase from Pseudomonas aeruginosa Authors: Nguyen, D.D. / Pandian, R. / Kim, D. / Ha, S.C. / Yoon, H.J. / Kim, K.S. / Yun, K.H. / Kim, J.H. / Kim, K.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 | ![]() | 328.7 KB | Display | ![]() |
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PDB format | ![]() | 269.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 461.7 KB | Display | ![]() |
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Full document | ![]() | 494 KB | Display | |
Data in XML | ![]() | 65.3 KB | Display | |
Data in CIF | ![]() | 91.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3wt4C ![]() 4njqSC ![]() 4njrC ![]() 4oiwC 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
#1: Protein | Mass: 46669.410 Da / Num. of mol.: 4 / Mutation: D236A Source method: isolated from a genetically manipulated source Details: Cytosolic proteins / Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q9HYZ3, Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.95 Å3/Da / Density % sol: 58.35 % |
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Crystal grow | Temperature: 295 K / pH: 8 Details: 30% PEG400, 0.1M Tris, 0.2M MgCl2, 0.1mM ZnCl2 , pH 8.0, Microbatch Crystallization, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 24, 2009 |
Radiation | Monochromator: VARIABLE-INCLUDED-ANGLE PLANE- GRATING MONOCHROMATOR Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.999999999 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 94682 / % possible obs: 86 % / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 2.3→2.5 Å / Redundancy: 3.5 % / % possible all: 98.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4NJQ Resolution: 2.3→31.88 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.934 / SU B: 4.707 / SU ML: 0.118 / Cross valid method: THROUGHOUT / ESU R: 0.225 / ESU R Free: 0.188 / 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: 26.86 Å2
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Refine analyze | Luzzati coordinate error obs: 0.031 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→31.88 Å
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Refine LS restraints |
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