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Yorodumi- PDB-5lrk: Crystal structure of the porcine carboxypeptidase B - Anabaenopep... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5lrk | |||||||||
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Title | Crystal structure of the porcine carboxypeptidase B - Anabaenopeptin F complex | |||||||||
Components |
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Keywords | HYDROLASE / Drug discovery / Natural compound / Tafi inhibitor / Anabaenopeptin | |||||||||
Function / homology | Function and homology information carboxypeptidase B / metallocarboxypeptidase activity / cytoplasmic vesicle / proteolysis / extracellular space / zinc ion binding Similarity search - Function | |||||||||
Biological species | Sus scrofa (pig) Planktothrix rubescens (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | |||||||||
Authors | Schreuder, H. / Liesum, A. / Loenze, P. | |||||||||
Citation | Journal: Sci Rep / Year: 2016 Title: Isolation, Co-Crystallization and Structure-Based Characterization of Anabaenopeptins as Highly Potent Inhibitors of Activated Thrombin Activatable Fibrinolysis Inhibitor (TAFIa). Authors: Schreuder, H. / Liesum, A. / Lonze, P. / Stump, H. / Hoffmann, H. / Schiell, M. / Kurz, M. / Toti, L. / Bauer, A. / Kallus, C. / Klemke-Jahn, C. / Czech, J. / Kramer, D. / Enke, H. / ...Authors: Schreuder, H. / Liesum, A. / Lonze, P. / Stump, H. / Hoffmann, H. / Schiell, M. / Kurz, M. / Toti, L. / Bauer, A. / Kallus, C. / Klemke-Jahn, C. / Czech, J. / Kramer, D. / Enke, H. / Niedermeyer, T.H. / Morrison, V. / Kumar, V. / Bronstrup, M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5lrk.cif.gz | 219 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5lrk.ent.gz | 173.2 KB | Display | PDB format |
PDBx/mmJSON format | 5lrk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lr/5lrk ftp://data.pdbj.org/pub/pdb/validation_reports/lr/5lrk | HTTPS FTP |
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-Related structure data
Related structure data | 5lrgC 5lrjC 1nsaS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 34739.859 Da / Num. of mol.: 3 / Fragment: UNP residues 111-416 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: P09955, carboxypeptidase B #2: Protein/peptide | Mass: 869.019 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Planktothrix rubescens (bacteria) / Strain: CBT287 #3: Chemical | #4: Water | ChemComp-HOH / | |
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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: 2.09 Å3/Da / Density % sol: 41.1 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 1ul of 16 mg/ml Protein and 40 mM epsilon-amino caproic acid in water were equilibrated against 14-20% PEG8000 and 100 mM K-Cacodylate (pH 6.5) in a hanging drop Setup. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 9, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→62.24 Å / Num. obs: 37153 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 2.9 % / Biso Wilson estimate: 25.3 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.8 |
Reflection shell | Resolution: 2.3→2.39 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.279 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1NSA Resolution: 2.3→62.24 Å / Data cutoff high absF: 10000 / Cross valid method: FREE R-VALUE / σ(F): 0
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Displacement parameters | Biso mean: 21.2 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→62.24 Å
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LS refinement shell | Resolution: 2.3→2.4 Å
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