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Yorodumi- PDB-1qtr: CRYSTAL STRUCTURE ANALYSIS OF THE PROLYL AMINOPEPTIDASE FROM SERR... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1qtr | ||||||
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Title | CRYSTAL STRUCTURE ANALYSIS OF THE PROLYL AMINOPEPTIDASE FROM SERRATIA MARCESCENS | ||||||
Components | PROLYL AMINOPEPTIDASE | ||||||
Keywords | HYDROLASE / ALPHA BETA HYDROLASE FOLD / PROLINE / PROLYL AMINOPEPTIDASE / SERRATIA / IMINOPEPTIDASE | ||||||
Function / homology | Function and homology information prolyl aminopeptidase / aminopeptidase activity / proteolysis / cytoplasm Similarity search - Function | ||||||
Biological species | Serratia marcescens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.32 Å | ||||||
Authors | Yoshimoto, T. / Kabashima, T. / Uchikawa, K. / Inoue, T. / Tanaka, N. | ||||||
Citation | Journal: J.Biochem.(Tokyo) / Year: 1999 Title: Crystal structure of prolyl aminopeptidase from Serratia marcescens. Authors: Yoshimoto, T. / Kabashima, T. / Uchikawa, K. / Inoue, T. / Tanaka, N. / Nakamura, K.T. / Tsuru, M. / Ito, K. #1: Journal: J.Biochem.(Tokyo) / Year: 1997 Title: Prolyl Aminopeptidase from Serratia marcescens : Sequencing and Expression Authors: Kabashima, T. / Kitazono, A. / Kitano, A. / Inoue, K. / Yoshimoto, T. #2: Journal: J.Biochem.(Tokyo) / Year: 1994 Title: Prolyl aminopeptidase is not a sulfhydryl enzyme: Identification of the active serine residue by site-directed mutagenesis Authors: Kitazono, A. / Ito, K. / Yoshimoto, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1qtr.cif.gz | 71.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qtr.ent.gz | 54.7 KB | Display | PDB format |
PDBx/mmJSON format | 1qtr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1qtr_validation.pdf.gz | 365.6 KB | Display | wwPDB validaton report |
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Full document | 1qtr_full_validation.pdf.gz | 376.4 KB | Display | |
Data in XML | 1qtr_validation.xml.gz | 9.1 KB | Display | |
Data in CIF | 1qtr_validation.cif.gz | 12.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qt/1qtr ftp://data.pdbj.org/pub/pdb/validation_reports/qt/1qtr | 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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-Components
#1: Protein | Mass: 36130.594 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Serratia marcescens (bacteria) / Plasmid: PSPAP-HE / Production host: Escherichia coli (E. coli) / References: UniProt: O32449, prolyl aminopeptidase |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.79 % | |||||||||||||||||||||||||
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG6000, SODIUM ACETATE, NA CACODYLATE/KH2PO4, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 297K | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Details: Kabashima, T., (1997) J.Biochem.(Tokyo), 122, 601. | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Oct 25, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.32→10 Å / Num. obs: 45646 / % possible obs: 89.1 % / Rmerge(I) obs: 0.059 |
Reflection | *PLUS Num. obs: 14917 / Num. measured all: 45646 |
-Processing
Software |
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Refinement | Resolution: 2.32→8 Å / σ(F): 1
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Refinement step | Cycle: LAST / Resolution: 2.32→8 Å
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||
Refine LS restraints | *PLUS
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