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- PDB-4tz3: Ensemble refinement of the E502A variant of sacteLam55A from Stre... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4tz3 | |||||||||
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Title | Ensemble refinement of the E502A variant of sacteLam55A from Streptomyces sp. SirexAA-E in complex with laminaritetraose | |||||||||
![]() | Putative secreted protein | |||||||||
![]() | 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![]() | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() ![]() | |||||||||
![]() | Bianchetti, C.M. / Takasuka, T.E. / Yik, E.J. / Bergeman, L.F. / Fox, B.G. | |||||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 8.6 MB | Display | ![]() |
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PDB format | ![]() | 7.3 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 5.2 MB | Display | ![]() |
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Full document | ![]() | 5.4 MB | Display | |
Data in XML | ![]() | 512.9 KB | Display | |
Data in CIF | ![]() | 752.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4pewSC ![]() 4pexC ![]() 4peyC ![]() 4pezC ![]() 4pf0C ![]() 4tyvC ![]() 4tz1C ![]() 4tz5C C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Number of models | 25 |
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Components
#1: Protein | Mass: 58884.359 Da / Num. of mol.: 1 / Fragment: UNP residues 57-605 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||
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#2: Polysaccharide | beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||
#3: Sugar | ChemComp-BGC / | ||
#4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 % / Rmerge(I) obs: 0.095 / Χ2: 0.908 / Net I/av σ(I): 11.767 / Net I/σ(I): 7.3 / Num. measured all: 191860 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4PEW Resolution: 1.9→28.332 Å / SU ML: 0.09 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 14.58 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso min: 99999 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.9→28.332 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14
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