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Open data
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Basic information
Entry | Database: PDB / ID: 1q7l | ||||||
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Title | Zn-binding domain of the T347G mutant of human aminoacylase-I | ||||||
![]() | (Aminoacylase-1) x 2 | ||||||
![]() | HYDROLASE / aminoacylase-1 / catalysis / enzyme dimerization / site-directed mutagenesis / structure comparison / zinc | ||||||
Function / homology | ![]() N-acyl-aliphatic-L-amino acid amidohydrolase / Defective ACY1 causes encephalopathy / aminoacylase activity / Aflatoxin activation and detoxification / amino acid metabolic process / xenobiotic metabolic process / extracellular exosome / identical protein binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lindner, H.A. / Lunin, V.V. / Alary, A. / Hecker, R. / Cygler, M. / Menard, R. | ||||||
![]() | ![]() Title: Essential roles of zinc ligation and enzyme dimerization for catalysis in the aminoacylase-1/M20 family. Authors: Lindner, H.A. / Lunin, V.V. / Alary, A. / Hecker, R. / Cygler, M. / Menard, R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 256.1 KB | Display | ![]() |
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PDB format | ![]() | 205.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 458.2 KB | Display | ![]() |
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Full document | ![]() | 462.5 KB | Display | |
Data in XML | ![]() | 29.3 KB | Display | |
Data in CIF | ![]() | 44.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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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Details | A dimer formed without dimerization domains. This dimer is not biologically relevant. |
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Components
#1: Protein | Mass: 22556.510 Da / Num. of mol.: 2 / Fragment: Zn-binding domain (residues 1-198) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q03154, N-acyl-aliphatic-L-amino acid amidohydrolase #2: Protein | Mass: 9792.244 Da / Num. of mol.: 2 / Fragment: residues 321-408 / Mutation: T347G Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q03154, N-acyl-aliphatic-L-amino acid amidohydrolase #3: Chemical | ChemComp-ZN / #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 39.59 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: PEG8000, (NH4)2SO4, CoCl2, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 20, 2002 |
Radiation | Monochromator: GRAPHITE / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.005685 Å / Relative weight: 1 |
Reflection | *PLUS Highest resolution: 1.5 Å / Lowest resolution: 50 Å / Num. obs: 158345 / % possible obs: 95.8 % / Num. measured all: 529534 / Rmerge(I) obs: 0.074 |
Reflection shell | *PLUS Highest resolution: 1.5 Å / Lowest resolution: 1.55 Å / % possible obs: 81.9 % / Rmerge(I) obs: 0.344 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.204 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→33.71 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.4→1.436 Å / Total num. of bins used: 20 /
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Refinement | *PLUS Highest resolution: 1.4 Å / Lowest resolution: 50 Å / Rfactor Rfree: 0.172 / Rfactor Rwork: 0.133 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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