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- PDB-1h4p: Crystal structure of exo-1,3-beta glucanse from Saccharomyces cer... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1h4p | ||||||||||||
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Title | Crystal structure of exo-1,3-beta glucanse from Saccharomyces cerevisiae | ||||||||||||
![]() | GLUCAN 1,3-BETA-GLUCOSIDASE I/II | ||||||||||||
![]() | HYDROLASE / GLUCAN DEGRADATION / HYDROLYASE / GLYCOSIDASE | ||||||||||||
Function / homology | ![]() : / glucan 1,3-beta-glucosidase / glucan exo-1,3-beta-glucosidase activity / fungal-type cell wall organization / fungal-type cell wall / glucan catabolic process / fungal-type vacuole / beta-glucosidase activity / cell surface / extracellular region Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Ferguson, A.D. | ||||||||||||
![]() | ![]() Title: The Er Protein Folding Sensor Udp-Glucose Glycoprotein:Glucosyltransferase Modifies Substrates Distant to Local Changes in Glycoprotein Conformation. Authors: Taylor, S.C. / Ferguson, A.D. / Bergeron, J.J.M. / Thomas, D.Y. | ||||||||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" AND "BA" IN EACH CHAIN ON SHEET ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" AND "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 194.6 KB | Display | ![]() |
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PDB format | ![]() | 154.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1cz1S 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.0276, -0.9949, 0.09705), Vector: |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 47003.746 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: TWO MAN9GLCNAC GLYCAN CHAINS ARE LOCATED AT RESIDUES N165 AND N325 Source: (gene. exp.) ![]() ![]() Production host: ![]() ![]() |
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-Sugars , 4 types, 4 molecules
#2: Polysaccharide | beta-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-beta-D- ...beta-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-beta-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[beta-D-mannopyranose-(1-2)-beta-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#3: Polysaccharide | beta-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...beta-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#4: Polysaccharide | beta-D-mannopyranose-(1-2)-beta-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-3)-[beta-D- ...beta-D-mannopyranose-(1-2)-beta-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#5: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
-Non-polymers , 2 types, 465 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#6: Chemical | ChemComp-GOL / #7: Water | ChemComp-HOH / | |
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-Details
Compound details | GLUCANASES |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.96 Å3/Da / Density % sol: 58 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 100 MM SODIUM HEPES PH 7.8, 25 MM MGCL2, 1.3 M TRI-SODIUM CITRATE, 20% GLYCEROL | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / pH: 8 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jul 15, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9786 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→50 Å / Num. obs: 104421 / % possible obs: 95 % / Redundancy: 12 % / Biso Wilson estimate: 21.8 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 37 |
Reflection shell | Resolution: 1.75→1.86 Å / Redundancy: 4 % / Rmerge(I) obs: 0.433 / Mean I/σ(I) obs: 2.8 / % possible all: 80 |
Reflection | *PLUS Highest resolution: 1.75 Å / % possible obs: 97.6 % / Num. measured all: 107423 / Rmerge(I) obs: 0.043 |
Reflection shell | *PLUS % possible obs: 86.9 % / Rmerge(I) obs: 0.443 / Mean I/σ(I) obs: 2.8 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1CZ1 Resolution: 1.75→36.27 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 416551.13 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 51.8131 Å2 / ksol: 0.407808 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.75→36.27 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.86 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Lowest resolution: 50 Å / % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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