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Yorodumi- PDB-1a5i: CATALYTIC DOMAIN OF VAMPIRE BAT (DESMODUS ROTUNDUS) SALIVA PLASMI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1a5i | ||||||
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Title | CATALYTIC DOMAIN OF VAMPIRE BAT (DESMODUS ROTUNDUS) SALIVA PLASMINOGEN ACTIVATOR IN COMPLEX WITH EGR-CMK (GLU-GLY-ARG CHLOROMETHYL KETONE) | ||||||
Components | PLASMINOGEN ACTIVATOR | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / SERINE PROTEASE / FIBRINOLYTIC ENZYMES / PLASMINOGEN ACTIVATORS / HYDROLASE-HYDROLASE INHIBITOR COMPLEX | ||||||
Function / homology | Function and homology information t-plasminogen activator / smooth muscle cell migration / plasminogen activation / serine-type endopeptidase activity / calcium ion binding / extracellular region Similarity search - Function | ||||||
Biological species | Desmodus rotundus (common vampire bat) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Renatus, M. / Stubbs, M.T. / Bode, W. | ||||||
Citation | Journal: Biochemistry / Year: 1997 Title: Catalytic domain structure of vampire bat plasminogen activator: a molecular paradigm for proteolysis without activation cleavage. Authors: Renatus, M. / Stubbs, M.T. / Huber, R. / Bringmann, P. / Donner, P. / Schleuning, W.D. / Bode, W. #1: Journal: Embo J. / Year: 1997 Title: Lysine 156 Promotes the Anomalous Proenzyme Activity of Tpa: X-Ray Crystal Structure of Single-Chain Human Tpa Authors: Renatus, M. / Engh, R.A. / Stubbs, M.T. / Huber, R. / Fischer, S. / Kohnert, U. / Bode, W. #2: Journal: Curr.Opin.Struct.Biol. / Year: 1997 Title: Tissue-Type Plasminogen Activator: Variants and Crystal/Solution Structures Demarcate Structural Determinants of Function Authors: Bode, W. / Renatus, M. #3: Journal: J.Mol.Biol. / Year: 1996 Title: The 2.3 A Crystal Structure of the Catalytic Domain of Recombinant Two-Chain Human Tissue-Type Plasminogen Activator Authors: Lamba, D. / Bauer, M. / Huber, R. / Fischer, S. / Rudolph, R. / Kohnert, U. / Bode, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1a5i.cif.gz | 62.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1a5i.ent.gz | 49.2 KB | Display | PDB format |
PDBx/mmJSON format | 1a5i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a5/1a5i ftp://data.pdbj.org/pub/pdb/validation_reports/a5/1a5i | HTTPS FTP |
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-Related structure data
Related structure data | 1rtfS S: Starting model for refinement |
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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: 29716.600 Da / Num. of mol.: 1 / Fragment: UNP residues 213-477 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Desmodus rotundus (common vampire bat) / Organ: SALIVARY GLANDS / Cell line (production host): BHK / Production host: Mesocricetus auratus (golden hamster) / References: UniProt: P98119, t-plasminogen activator |
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#2: Chemical | ChemComp-0GJ / |
#3: Water | ChemComp-HOH / |
Nonpolymer details | THE UNBOUND FORM OF THE INHIBITOR IS GLU-GLY-ARG-CHLOROMETHYLKETONE. UPON REACTION WITH PROTEIN IT ...THE UNBOUND FORM OF THE INHIBITOR IS GLU-GLY-ARG-CHLOROMETH |
Sequence details | THE PROTEIN IS A DELETION MUTANT OF FULL-LENGTH DSPAALPHA1 (P98119) CONSISTING OF A SIGNAL PEPTIDE ...THE PROTEIN IS A DELETION MUTANT OF FULL-LENGTH DSPAALPHA1 (P98119) CONSISTING |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.58 Å3/Da / Density % sol: 65.66 % | |||||||||||||||
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Crystal grow | pH: 9 / Details: pH 9.0 | |||||||||||||||
Crystal | *PLUS Density % sol: 59 % | |||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion, sitting drop / PH range low: 9.2 / PH range high: 8.8 | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 290 K |
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Diffraction source | Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 18, 1996 |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→25 Å / Num. obs: 9582 / % possible obs: 97.2 % / Observed criterion σ(I): 3 / Redundancy: 2.3 % / Biso Wilson estimate: 65.48 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 3.51 |
Reflection shell | Resolution: 2.9→3 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.405 / Mean I/σ(I) obs: 1.9 / % possible all: 97.9 |
Reflection | *PLUS Num. measured all: 22337 |
Reflection shell | *PLUS % possible obs: 97.9 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1RTF Resolution: 2.9→7 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / σ(F): 2
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Displacement parameters | Biso mean: 29 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→7 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→3 Å / Total num. of bins used: 10
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.3489 |