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Yorodumi- PDB-2vy0: The X-ray structure of endo-beta-1,3-glucanase from Pyrococcus fu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2vy0 | ||||||
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Title | The X-ray structure of endo-beta-1,3-glucanase from Pyrococcus furiosus | ||||||
Components | ENDO-BETA-1,3-GLUCANASE | ||||||
Keywords | HYDROLASE / LAMINARIN / ENDOGLUCANASE / THERMOSTABLE PROTEIN | ||||||
Function / homology | Function and homology information hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process / metal ion binding Similarity search - Function | ||||||
Biological species | PYROCOCCUS FURIOSUS (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.16 Å | ||||||
Authors | Ilari, A. / Fiorillo, A. | ||||||
Citation | Journal: FEBS J. / Year: 2009 Title: Crystal Structure of a Family 16 Endoglucanase from the Hyperthermophile Pyrococcus Furiosus-Structural Basis of Substrate Recognition. Authors: Ilari, A. / Fiorillo, A. / Angelaccio, S. / Florio, R. / Chiaraluce, R. / Van Der Oost, J. / Consalvi, V. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2vy0.cif.gz | 127.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vy0.ent.gz | 97.8 KB | Display | PDB format |
PDBx/mmJSON format | 2vy0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vy/2vy0 ftp://data.pdbj.org/pub/pdb/validation_reports/vy/2vy0 | HTTPS FTP |
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-Related structure data
Related structure data | 2hykS 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper: (Code: given Matrix: (-0.98563, -0.09663, -0.13854), Vector: |
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 30143.939 Da / Num. of mol.: 2 / Fragment: RESIDUES 35-297 Source method: isolated from a genetically manipulated source Source: (gene. exp.) PYROCOCCUS FURIOSUS (archaea) / Plasmid: PLUW530 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: O73951, glucan endo-1,3-beta-D-glucosidase |
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-Non-polymers , 6 types, 264 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | #7: 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: 2.2 Å3/Da / Density % sol: 43 % / Description: NONE |
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Crystal grow | pH: 7.5 Details: 0.1M HEPES [N-(2-HYDROXYETHYL)PIPERAZINE-N-2-ETHANESULFONIC ACID]PH 7.5-8.0 MPD (2-METHYL-2,4-PENTANEDIOL) 60%-70% |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 |
Detector | Type: MARRESEARCH / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→50 Å / Num. obs: 25211 / % possible obs: 99.8 % / Redundancy: 7 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 13.4 |
Reflection shell | Resolution: 2.15→2.23 Å / Redundancy: 3 % / Rmerge(I) obs: 0.21 / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2HYK Resolution: 2.16→50 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.92 / SU B: 5.578 / SU ML: 0.146 / Cross valid method: THROUGHOUT / ESU R: 0.35 / ESU R Free: 0.216 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.47 Å2
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Refinement step | Cycle: LAST / Resolution: 2.16→50 Å
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Refine LS restraints |
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