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Yorodumi- PDB-1wm1: Crystal Structure of Prolyl Aminopeptidase, Complex with Pro-TBODA -
+Open data
-Basic information
Entry | Database: PDB / ID: 1wm1 | ||||||
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Title | Crystal Structure of Prolyl Aminopeptidase, Complex with Pro-TBODA | ||||||
Components | Proline iminopeptidase | ||||||
Keywords | HYDROLASE / proline iminopeptidase / complex with inhibitor | ||||||
Function / homology | Function and homology information prolyl aminopeptidase / aminopeptidase activity / proteolysis / cytoplasm Similarity search - Function | ||||||
Biological species | Serratia marcescens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.1 Å | ||||||
Authors | Nakajima, Y. / Inoue, T. / Ito, K. / Tozaka, T. / Hatakeyama, S. / Tanaka, N. / Nakamura, K.T. / Yoshimoto, T. | ||||||
Citation | Journal: ARCH.BIOCHEM.BIOPHYS. / Year: 2003 Title: Novel inhibitor for prolyl aminopeptidase from Serratia marcescens and studies on the mechanism of substrate recognition of the enzyme using the inhibitor Authors: Inoue, T. / Ito, K. / Tozaka, T. / Hatakeyama, S. / Tanaka, N. / Nakamura, K.T. / Yoshimoto, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1wm1.cif.gz | 75.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1wm1.ent.gz | 56.3 KB | Display | PDB format |
PDBx/mmJSON format | 1wm1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1wm1_validation.pdf.gz | 450.6 KB | Display | wwPDB validaton report |
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Full document | 1wm1_full_validation.pdf.gz | 456.7 KB | Display | |
Data in XML | 1wm1_validation.xml.gz | 14.8 KB | Display | |
Data in CIF | 1wm1_validation.cif.gz | 19.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wm/1wm1 ftp://data.pdbj.org/pub/pdb/validation_reports/wm/1wm1 | HTTPS FTP |
-Related structure data
Related structure data | |
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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: 36130.594 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Serratia marcescens (bacteria) / Plasmid: pUC19 / Production host: Escherichia coli (E. coli) / References: UniProt: O32449, prolyl aminopeptidase |
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#2: Chemical | ChemComp-PTB / ( |
#3: 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: 2.51 Å3/Da / Density % sol: 51 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG6000, cacodylate, sodium acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 17, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→40 Å / Num. all: 22338 / Num. obs: 22338 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Rsym value: 0.042 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 2.1→2.21 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 3.2 / Num. unique all: 3194 / Rsym value: 0.228 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 2.1→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.18 Å
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