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Yorodumi- PDB-4ns4: Crystal structure of cold-active estarase from Psychrobacter cryo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ns4 | ||||||
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Title | Crystal structure of cold-active estarase from Psychrobacter cryohalolentis K5T | ||||||
Components | Alpha/beta hydrolase fold protein | ||||||
Keywords | HYDROLASE / alpha/beta hydrolase fold / cold-active esterase | ||||||
Function / homology | hydrolase activity, acting on ester bonds / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Alpha/beta hydrolase fold protein Function and homology information | ||||||
Biological species | Psychrobacter cryohalolentis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | ||||||
Authors | Boyko, K.M. / Petrovskaya, L.E. / Gorbacheva, M.A. / Korgenevsky, D.A. / Novototskaya-Vlasova, K.A. / Rivkina, E.M. / Dolgikh, D.A. / Kirpichnikov, M.P. / Lipkin, A.V. / Popov, V.O. | ||||||
Citation | Journal: To be Published Title: Three-dimentional structure of an esterse from Psychrobacter cryohalolentis K5T provides clues to unusual thermostability of a cold-active enzyme Authors: Boyko, K.M. / Petrovskaya, L.E. / Gorbacheva, M.A. / Korgenevsky, D.A. / Novototskaya-Vlasova, K.A. / Rivkina, E.M. / Dolgikh, D.A. / Kirpichnikov, M.P. / Lipkin, A.V. / Popov, V.O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ns4.cif.gz | 69.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ns4.ent.gz | 50.6 KB | Display | PDB format |
PDBx/mmJSON format | 4ns4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ns4_validation.pdf.gz | 428.6 KB | Display | wwPDB validaton report |
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Full document | 4ns4_full_validation.pdf.gz | 433.9 KB | Display | |
Data in XML | 4ns4_validation.xml.gz | 13.9 KB | Display | |
Data in CIF | 4ns4_validation.cif.gz | 19.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ns/4ns4 ftp://data.pdbj.org/pub/pdb/validation_reports/ns/4ns4 | HTTPS FTP |
-Related structure data
Related structure data | 1j1iS 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: 35658.773 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Psychrobacter cryohalolentis (bacteria) Strain: K5T / Gene: Pcryo_0023 / Plasmid: pET32a(+)/EstPc / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q1QEU6, acetylesterase |
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#2: 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: 2.34 Å3/Da / Density % sol: 47.36 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1M HEPES, 14% PEG4000, 10% 2-propanol, 15% glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: KURCHATOV SNC / Beamline: K4.4 / Wavelength: 0.984 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Apr 19, 2012 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.984 Å / Relative weight: 1 |
Reflection | Resolution: 2.12→30 Å / Num. all: 19420 / Num. obs: 19246 / % possible obs: 99.1 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 |
Reflection shell | Resolution: 2.12→2.25 Å / % possible all: 95.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1J1I Resolution: 2.15→28.59 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.918 / SU B: 5.35 / SU ML: 0.139 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.208 / ESU R Free: 0.198 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.556 Å2
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Refinement step | Cycle: LAST / Resolution: 2.15→28.59 Å
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Refine LS restraints |
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