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Yorodumi- PDB-5mrs: Crystal structure of L1 protease Lysobacter sp. XL1 in complex wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5mrs | ||||||
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Title | Crystal structure of L1 protease Lysobacter sp. XL1 in complex with AEBSF | ||||||
Components | Lytic endopeptidase preproenzyme | ||||||
Keywords | HYDROLASE / Bacteriolytic protease L1 / Lysobacter sp. XL1 / Crystals / AEBSF | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Lysobacter sp. | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Gabdulkhakov, A. / Tishchenko, S. / Lisov, A. / Leontievsky, A. | ||||||
Citation | Journal: To Be Published Title: Crystal structure of L1 protease Lysobacter sp. XL1 in complex with AEBSF Authors: Gabdulkhakov, A. / Tishchenko, S. / Lisov, A. / Leontievsky, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5mrs.cif.gz | 165 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5mrs.ent.gz | 130.3 KB | Display | PDB format |
PDBx/mmJSON format | 5mrs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mr/5mrs ftp://data.pdbj.org/pub/pdb/validation_reports/mr/5mrs | HTTPS FTP |
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-Related structure data
Related structure data | 5mrrS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 19848.051 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lysobacter sp. (strain XL1) (bacteria) / Gene: alpA / Production host: Escherichia coli (E. coli) / References: UniProt: D2K8B3 |
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-Non-polymers , 7 types, 332 molecules
#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-AES / #4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-PGE / | #6: Chemical | #7: Chemical | ChemComp-PEG / #8: 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: 2.52 Å3/Da / Density % sol: 51.24 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 1,4M Lithium sulphate, 0,1M BisTris, |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.96863 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 10, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96863 Å / Relative weight: 1 |
Reflection | Resolution: 1.86→50 Å / Num. obs: 65564 / % possible obs: 99.4 % / Redundancy: 4.75 % / Net I/σ(I): 8.13 |
Reflection shell | Resolution: 1.86→1.97 Å / Mean I/σ(I) obs: 1.7 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5MRR Resolution: 1.9→48.207 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.29 / Phase error: 26.68
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→48.207 Å
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Refine LS restraints |
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LS refinement shell |
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