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Yorodumi- PDB-4pez: Structure of the E502A variant of sacteLam55A from Streptomyces s... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4pez | |||||||||
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Title | Structure of the E502A variant of sacteLam55A from Streptomyces sp. SirexAA-E in complex with laminaritetraose | |||||||||
Components | Putative secreted proteinSecretory protein | |||||||||
Keywords | HYDROLASE / exo-beta-1 / 3-glucanase / beta-1 / GH55 / laminaritetraose / 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: 1.9 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 | 4pez.cif.gz | 134.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4pez.ent.gz | 99.7 KB | Display | PDB format |
PDBx/mmJSON format | 4pez.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pe/4pez ftp://data.pdbj.org/pub/pdb/validation_reports/pe/4pez | HTTPS FTP |
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-Related structure data
Related structure data | 4pewC 4pexC 4peyC 4pf0C 4tyvC 4tz1C 4tz3C 4tz5C C: citing same article (ref.) |
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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: 60072.637 Da / Num. of mol.: 1 / Fragment: UNP residues 46-605 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 | ||
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#2: Polysaccharide | beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose | ||
#3: Sugar | ChemComp-BGC / | ||
#4: Chemical | #5: 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: 47.29 % |
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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 (22% PEG 3350, 50mM NaCH02, and 100mM BTP pH 6.5). Cryoprotected with 22% ...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 (22% PEG 3350, 50mM NaCH02, and 100mM BTP pH 6.5). Cryoprotected with 22% PEG 3350, 50mM NaCH02, 25mM laminaritetraose, 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 | Redundancy: 3.9 % / Number: 191860 / Rmerge(I) obs: 0.095 / Χ2: 0.91 / D res high: 1.8 Å / D res low: 50 Å / Num. obs: 49764 / % possible obs: 99.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 1.8→50 Å / Num. obs: 49764 / % possible obs: 99.2 % / Redundancy: 3.9 % / Biso Wilson estimate: 20.19 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 7.3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Resolution: 1.8→1.83 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.565 / % possible all: 98.9 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→28.33 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 17.03 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→28.33 Å
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Refine LS restraints |
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LS refinement shell |
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