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Yorodumi- PDB-1igb: AEROMONAS PROTEOLYTICA AMINOPEPTIDASE COMPLEXED WITH THE INHIBITO... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1igb | ||||||
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Title | AEROMONAS PROTEOLYTICA AMINOPEPTIDASE COMPLEXED WITH THE INHIBITOR PARA-IODO-D-PHENYLALANINE HYDROXAMATE | ||||||
Components | AMINOPEPTIDASE | ||||||
Keywords | AMINOPEPTIDASE / HYDROLASE | ||||||
Function / homology | Function and homology information bacterial leucyl aminopeptidase / metalloexopeptidase activity / aminopeptidase activity / proteolysis / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | Vibrio proteolyticus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT SOFTWARE USED : X-PLOR STARTING MODEL FOR MOLECULAR REPLACEMENT: NATIVE PROTEIN (REFERENCE 1) / Resolution: 2.3 Å | ||||||
Authors | Chevrier, B. / D'Orchymont, H. / Schalk, C. / Tarnus, C. / Moras, D. | ||||||
Citation | Journal: Eur.J.Biochem. / Year: 1996 Title: The structure of the Aeromonas proteolytica aminopeptidase complexed with a hydroxamate inhibitor. Involvement in catalysis of Glu151 and two zinc ions of the co-catalytic unit. Authors: Chevrier, B. / D'Orchymont, H. / Schalk, C. / Tarnus, C. / Moras, D. #1: Journal: Structure / Year: 1994 Title: Crystal Structure of Aeromonas Proteolytica Aminopeptidase: A Prototypical Member of the Co-Catalytic Zinc Enzyme Family Authors: Chevrier, B. / Schalk, C. / D'Orchymont, H. / Rondeau, J.M. / Moras, D. / Tarnus, C. #2: Journal: Arch.Biochem.Biophys. / Year: 1992 Title: Rapid Purification of the Aeromonas Proteolytica Aminopeptidase: Crystallization and Preliminary X-Ray Data Authors: Schalk, C. / Remy, J.M. / Chevrier, B. / Moras, D. / Tarnus, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1igb.cif.gz | 87.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1igb.ent.gz | 71.7 KB | Display | PDB format |
PDBx/mmJSON format | 1igb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1igb_validation.pdf.gz | 694.6 KB | Display | wwPDB validaton report |
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Full document | 1igb_full_validation.pdf.gz | 700.9 KB | Display | |
Data in XML | 1igb_validation.xml.gz | 15.9 KB | Display | |
Data in CIF | 1igb_validation.cif.gz | 23 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ig/1igb ftp://data.pdbj.org/pub/pdb/validation_reports/ig/1igb | 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: 31427.350 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vibrio proteolyticus (bacteria) References: UniProt: Q01693, bacterial leucyl aminopeptidase | ||||
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#2: Chemical | #3: Chemical | ChemComp-IPO / | #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: 2.69 Å3/Da / Density % sol: 54.27 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 7 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 291 K |
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Diffraction source | Source: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418 |
Detector | Type: XENTRONICS / Detector: AREA DETECTOR / Date: Sep 1, 1993 |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 15274 / % possible obs: 91.7 % / Observed criterion σ(I): 0 / Redundancy: 7.7 % / Rmerge(I) obs: 0.081 |
Reflection | *PLUS Num. measured all: 118144 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT SOFTWARE USED : X-PLOR STARTING MODEL FOR MOLECULAR REPLACEMENT: NATIVE PROTEIN (REFERENCE 1) Resolution: 2.3→8 Å / σ(F): 2
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Displacement parameters | Biso mean: 15.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.01 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→8 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.16 / Rfactor Rwork: 0.16 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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