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- PDB-1v4y: The functional role of the binuclear metal center in D-aminoacyla... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1v4y | ||||||
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Title | The functional role of the binuclear metal center in D-aminoacylase. One-metal activation and second-metal attenuation | ||||||
![]() | D-aminoacylase | ||||||
![]() | HYDROLASE / TIM barrel / beta barrel / insertion | ||||||
Function / homology | ![]() N-acyl-D-amino-acid deacylase / N-acyl-D-amino-acid deacylase activity / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lai, W.L. / Chou, L.Y. / Ting, C.Y. / Tsai, Y.C. / Liaw, S.H. | ||||||
![]() | ![]() Title: The Functional Role of the Binuclear Metal Center in D-Aminoacylase: ONE-METAL ACTIVATION AND SECOND-METAL ATTENUATION. Authors: Lai, W.L. / Chou, L.Y. / Ting, C.Y. / Kirby, R. / Tsai, Y.C. / Wang, A.H. / Liaw, S.H. #1: ![]() Title: Crystal structure of D-aminoacylase from Alcaligenes faecalis DA1. A novel subset of amidohydrolases and insights into the enzyme mechanism Authors: Liaw, S.H. / Chen, S.J. / Ko, T.P. / Hsu, C.S. / Chen, C.J. / Wang, A.H. / Tsai, Y.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 | ![]() | 110.4 KB | Display | ![]() |
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PDB format | ![]() | 81.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 434.9 KB | Display | ![]() |
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Full document | ![]() | 436.9 KB | Display | |
Data in XML | ![]() | 21.1 KB | Display | |
Data in CIF | ![]() | 31.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1rjpC ![]() 1rjqC ![]() 1rjrC ![]() 1rk5C ![]() 1rk6C ![]() 1v51C ![]() 1m7jS 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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Unit cell |
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Components
#1: Protein | Mass: 53399.168 Da / Num. of mol.: 1 / Mutation: H220A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-ACT / |
#3: Chemical | ChemComp-ZN / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.85 Å3/Da / Density % sol: 56.47 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: PEG400, ammonium acetate, sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 5, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→50 Å / Num. obs: 73452 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.2 % / Rmerge(I) obs: 0.089 / Rsym value: 0.075 / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 1.65→1.68 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.327 / Mean I/σ(I) obs: 2.5 / Num. unique all: 3024 / Rsym value: 0.378 / % possible all: 80.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1M7J Resolution: 1.65→36.07 Å / Isotropic thermal model: Anisotropic B / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 15.4 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→36.07 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 2
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