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Yorodumi- PDB-1m7j: Crystal structure of D-aminoacylase defines a novel subset of ami... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1m7j | ||||||
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Title | Crystal structure of D-aminoacylase defines a novel subset of amidohydrolases | ||||||
Components | D-aminoacylase | ||||||
Keywords | HYDROLASE / TIN-barrel / metal-dependent amidohydrolase | ||||||
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 / SAD / Resolution: 1.5 Å | ||||||
Authors | Liaw, S.-H. / Chen, S.-J. / Ko, T.-P. / Hsu, C.-S. / Wang, A.H.-J. / Tsai, Y.-C. | ||||||
Citation | 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. #1: 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. #2: Journal: Acta Crystallogr.,Sect.D / Year: 2002 Title: Crystallization and preliminary crystallographic analysis of a D-aminoacylase from Alcaligenes faecalis DA1 Authors: Hsu, C.-S. / Chen, S.-J. / Tsai, Y.-C. / Lin, T.-W. / Liaw, S.-H. / Wang, A.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1m7j.cif.gz | 114.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1m7j.ent.gz | 85.8 KB | Display | PDB format |
PDBx/mmJSON format | 1m7j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1m7j_validation.pdf.gz | 423.7 KB | Display | wwPDB validaton report |
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Full document | 1m7j_full_validation.pdf.gz | 425 KB | Display | |
Data in XML | 1m7j_validation.xml.gz | 22.9 KB | Display | |
Data in CIF | 1m7j_validation.cif.gz | 36 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m7/1m7j ftp://data.pdbj.org/pub/pdb/validation_reports/m7/1m7j | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | This protein is monomeric. |
-Components
#1: Protein | Mass: 52060.707 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Alcaligenes faecalis (bacteria) / Plasmid: pQE / 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 | #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: 2.74 Å3/Da / Density % sol: 54.79 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: sodium citrate, ammonium acetate, PEG 4000, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Details: Hsu, C.-S., (2002) Acta Crystallogr., Sect.D, 58, 1482. | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation | Monochromator: rotated-inclined double-crystal monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.5→50 Å / Num. all: 101683 / Num. obs: 100783 / % possible obs: 99.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6.3 % / Rmerge(I) obs: 0.047 / Net I/σ(I): 50.5 | |||||||||||||||
Reflection shell | Resolution: 1.5→1.55 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.116 / Mean I/σ(I) obs: 17.6 / Num. unique all: 9984 / % possible all: 100 | |||||||||||||||
Reflection | *PLUS Lowest resolution: 150 Å | |||||||||||||||
Reflection shell | *PLUS Highest resolution: 1.5 Å / % possible obs: 100 % / Num. unique obs: 9984 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.5→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 10.8 Å2 | |||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.5→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.55 Å
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Refinement | *PLUS Lowest resolution: 150 Å / Rfactor Rwork: 0.16 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS |