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Yorodumi- PDB-1v51: The functional role of the binuclear metal center in D-aminoacyla... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1v51 | ||||||
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Title | The functional role of the binuclear metal center in D-aminoacylase. One-metal activation and second-metal attenuation | ||||||
Components | D-aminoacylase | ||||||
Keywords | HYDROLASE / TIM barrel / beta barrel / insertion | ||||||
Function / homology | Function and homology information N-acyl-D-amino-acid deacylase / N-acyl-D-amino-acid deacylase activity / metal ion binding Similarity search - Function | ||||||
Biological species | Alcaligenes faecalis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Lai, W.L. / Chou, L.Y. / Ting, C.Y. / Tsai, Y.C. / Liaw, S.H. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2004 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: Journal: J.Biol.Chem. / Year: 2003 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. #2: Journal: Protein Sci. / Year: 2002 Title: Structural-based mutational analysis of D-aminoacylase from Alcaligenes faecalis DA1 Authors: Hsu, C.S. / Lai, W.L. / Chang, W.W. / Liaw, S.H. / Tsai, Y.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1v51.cif.gz | 111 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1v51.ent.gz | 82.3 KB | Display | PDB format |
PDBx/mmJSON format | 1v51.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1v51_validation.pdf.gz | 434.8 KB | Display | wwPDB validaton report |
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Full document | 1v51_full_validation.pdf.gz | 435.6 KB | Display | |
Data in XML | 1v51_validation.xml.gz | 20.2 KB | Display | |
Data in CIF | 1v51_validation.cif.gz | 29.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v5/1v51 ftp://data.pdbj.org/pub/pdb/validation_reports/v5/1v51 | HTTPS FTP |
-Related structure data
Related structure data | 1rjpC 1rjqC 1rjrC 1rk5C 1rk6C 1v4yC 1m7jS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 53466.234 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Alcaligenes faecalis (bacteria) / Gene: DA1 / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): M15 / References: UniProt: Q9AGH8, N-acyl-D-amino-acid deacylase | ||||
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#2: Chemical | #3: Chemical | ChemComp-ZN / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.1 Å3/Da / Density % sol: 59.99 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: PEG4000, 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: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 29, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. all: 199812 / Num. obs: 73910 / % possible obs: 88.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Rmerge(I) obs: 0.078 / Rsym value: 0.093 / Net I/σ(I): 21.2 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 2 % / Rmerge(I) obs: 0.154 / Mean I/σ(I) obs: 5 / Num. unique all: 5817 / Rsym value: 0.234 / % possible all: 70.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1M7J Resolution: 1.6→25.4 Å / Isotropic thermal model: isotropic B / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 11.68 Å2 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→25.4 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.66 Å
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