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Yorodumi- PDB-4tyv: Ensemble refinement of the E502A variant of sacteLam55A from Stre... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4tyv | |||||||||
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Title | Ensemble refinement of the E502A variant of sacteLam55A from Streptomyces sp. SirexAA-E in complex with glucose | |||||||||
Components | Putative secreted proteinSecretory protein | |||||||||
Keywords | HYDROLASE / exo-beta-1 / 3-glucanase / beta-1 / GH55 / glucose / secreted / biomass degradation | |||||||||
Function / homology | glucan 1,3-beta-glucosidase / glucan exo-1,3-beta-glucosidase activity / glucan catabolic process / Pectin lyase fold / extracellular region / beta-D-glucopyranose / Exo-beta-1,3-glucanase Function and homology information | |||||||||
Biological species | Streptomyces sp. SirexAA-E (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 Å | |||||||||
Authors | Bianchetti, C.M. / Takasuka, T.E. / Yik, E.J. / Bergeman, L.F. / Fox, B.G. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2015 Title: Active site and laminarin binding in glycoside hydrolase family 55. Authors: Bianchetti, C.M. / Takasuka, T.E. / Deutsch, S. / Udell, H.S. / Yik, E.J. / Bergeman, L.F. / Fox, B.G. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4tyv.cif.gz | 17 MB | Display | PDBx/mmCIF format |
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PDB format | pdb4tyv.ent.gz | 14.5 MB | Display | PDB format |
PDBx/mmJSON format | 4tyv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ty/4tyv ftp://data.pdbj.org/pub/pdb/validation_reports/ty/4tyv | HTTPS FTP |
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-Related structure data
Related structure data | 4pewSC 4pexC 4peyC 4pezC 4pf0C 4tz1C 4tz3C 4tz5C C: citing same article (ref.) 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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Number of models | 25 |
-Components
#1: Protein | Mass: 59083.562 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces sp. SirexAA-E (bacteria) / Gene: SACTE_4363 / Plasmid: PVP67K / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: G2NFJ9 #2: Chemical | ChemComp-EDO / #3: Sugar | ChemComp-BGC / | #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: 2.27 Å3/Da / Density % sol: 45.85 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: Protein Solution (20 mg/ml protein, 0.05 M NaCl, and 0.010 M MOPS pH 7) mixed in a 1:1 ratio with the Well Solution (20% PEG 3350, 125mM NaCH02, and 100mM BTP pH 6.5). Cryoprotected with 20% ...Details: Protein Solution (20 mg/ml protein, 0.05 M NaCl, and 0.010 M MOPS pH 7) mixed in a 1:1 ratio with the Well Solution (20% PEG 3350, 125mM NaCH02, and 100mM BTP pH 6.5). Cryoprotected with 20% PEG 3350, 125mM NaCH02, 75mM Glucose, 100mM BTP pH 6.5 and 15% ethylene glycol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 8, 2013 / Details: mirrors and beryllium lenses |
Radiation | Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 |
Reflection | Resolution: 1.66→50 Å / Num. obs: 123726 / % possible obs: 99.9 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 7.2 |
Reflection shell | Resolution: 1.66→1.69 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.546 / % possible all: 100 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4PEW Resolution: 1.75→24.27 Å / SU ML: 0.07 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 14.57 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→24.27 Å
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LS refinement shell |
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