+Open data
-Basic information
Entry | Database: PDB / ID: 5lyd | ||||||
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Title | Crystal structure of 1 in complex with tafCPB | ||||||
Components | Carboxypeptidase B | ||||||
Keywords | HYDROLASE / tafinized carboxypeptidase B | ||||||
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) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.02 Å | ||||||
Authors | Schreuder, H. / Liesum, A. / Loenze, P. | ||||||
Citation | Journal: J. Med. Chem. / Year: 2016 Title: Sulfamide as Zinc Binding Motif in Small Molecule Inhibitors of Activated Thrombin Activatable Fibrinolysis Inhibitor (TAFIa). Authors: Halland, N. / Czech, J. / Czechtizky, W. / Evers, A. / Follmann, M. / Kohlmann, M. / Schreuder, H.A. / Kallus, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5lyd.cif.gz | 79.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5lyd.ent.gz | 62.7 KB | Display | PDB format |
PDBx/mmJSON format | 5lyd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ly/5lyd ftp://data.pdbj.org/pub/pdb/validation_reports/ly/5lyd | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 34859.969 Da / Num. of mol.: 1 Mutation: F175I, T302S, M309H, L311V, I355L, P357L, A359P and S362G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sus scrofa (pig) / Gene: CPB1, CPB / Production host: Komagataella pastoris CBS 7435 (fungus) / References: UniProt: P09955, carboxypeptidase B | ||||
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#2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-7B0 / ( | #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: 2.33 Å3/Da / Density % sol: 47.2 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: THE PURIFIED PROTEIN WAS DISSOLVED IN 50 MM TRIS-HCL, PH 7.5 AND CONCENTRATED TO 11 MG/ML. 1 UL OF PROTEIN SOLUTION WAS EQUILIBRATED AGAINST 1 UL OF RESERVOIR SOLUTIONS CONTAINING 16-20% ...Details: THE PURIFIED PROTEIN WAS DISSOLVED IN 50 MM TRIS-HCL, PH 7.5 AND CONCENTRATED TO 11 MG/ML. 1 UL OF PROTEIN SOLUTION WAS EQUILIBRATED AGAINST 1 UL OF RESERVOIR SOLUTIONS CONTAINING 16-20% PEG3350, 100 mM MES PH 5.5 AND 50 mM ZnAcetate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.93 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 15, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.93 Å / Relative weight: 1 |
Reflection | Resolution: 2.02→62.26 Å / Num. obs: 22019 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Biso Wilson estimate: 41.5 Å2 / Rsym value: 0.073 / Net I/σ(I): 14.19 |
Reflection shell | Resolution: 2.02→2.08 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.466 / Mean I/σ(I) obs: 4.42 / % possible all: 100 |
-Processing
Software |
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Refinement | Resolution: 2.02→21.93 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.958 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.181 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.211 / SU Rfree Blow DPI: 0.148 / SU Rfree Cruickshank DPI: 0.14
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Displacement parameters | Biso mean: 41.84 Å2
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Refine analyze | Luzzati coordinate error obs: 0.23 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.02→21.93 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.02→2.12 Å / Rfactor Rfree error: 0 / Total num. of bins used: 11
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