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- PDB-1iex: Crystal structure of barley beta-D-glucan glucohydrolase isoenzym... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1iex | |||||||||
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Title | Crystal structure of barley beta-D-glucan glucohydrolase isoenzyme Exo1 in complex with 4I,4III,4V-S-trithiocellohexaose | |||||||||
![]() | BETA-D-GLUCAN GLUCOHYDROLASE ISOENZYME EXO1 | |||||||||
![]() | HYDROLASE / 2-domain fold | |||||||||
Function / homology | ![]() glucan catabolic process / beta-glucosidase / beta-glucosidase activity / extracellular region Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Hrmova, M. / DeGori, R. / Fincher, G.B. / Smith, B.J. / Driguez, H. / Varghese, J.N. | |||||||||
![]() | ![]() Title: Catalytic mechanisms and reaction intermediates along the hydrolytic pathway of a plant beta-D-glucan glucohydrolase. Authors: Hrmova, M. / Varghese, J.N. / De Gori, R. / Smith, B.J. / Driguez, H. / Fincher, G.B. | |||||||||
History |
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Remark 600 | HETEROGEN The ligand 4I,4III,4V-S-trithiocellohexaose is present in the crystal. Only the ...HETEROGEN The ligand 4I,4III,4V-S-trithiocellohexaose is present in the crystal. Only the thiocellobiose portion of the ligand is seen in the density; the 4III,4V-S-thiocellotetraose moiety is disordered and can not be seen. | |||||||||
Remark 999 | SEQUENCE The sequence in the GenBank entry might be a sequencing error at residue 345. The electron ...SEQUENCE The sequence in the GenBank entry might be a sequencing error at residue 345. The electron density unambiguously proved the presence of LYS instead of ASN at this residue. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 137.4 KB | Display | ![]() |
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PDB format | ![]() | 104.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 521.9 KB | Display | ![]() |
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Full document | ![]() | 531.2 KB | Display | |
Data in XML | ![]() | 14.4 KB | Display | |
Data in CIF | ![]() | 22.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1ieqC ![]() 1ievC ![]() 1iewC ![]() 1ex1S S: Starting model for refinement C: citing same article ( |
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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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Details | The biological assembly is a monomer constructed from an (alpha/beta)8 barrel and an (alpha/beta)6 sandwich. |
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Components
#1: Protein | Mass: 65475.617 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: GenBank: 4566505, UniProt: Q9XEI3*PLUS, glucan 1,3-beta-glucosidase |
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#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#3: Polysaccharide | beta-D-glucopyranose-(1-4)-4-thio-beta-D-glucopyranose / thio-beta-cellobiose |
#4: Sugar | ChemComp-NAG / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.71 Å3/Da / Density % sol: 66.87 % | ||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: ammonium sulfate, PEG 400, sodium acetate, Hepes-NaOH, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 277-279 K / Details: Hrmova, M., (1998) Acta Cryst., D54, 687. | ||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 255 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: WEISSENBERG / Detector: DIFFRACTOMETER / Date: Mar 1, 1998 / Details: Collimator |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→20 Å / Num. all: 123698 / Num. obs: 46444 / % possible obs: 83.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 15.8 |
Reflection shell | Resolution: 2.2→20 Å / Rmerge(I) obs: 0.486 / % possible all: 55.8 |
Reflection | *PLUS Redundancy: 4.4 % / Num. measured all: 123698 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1EX1 Resolution: 2.2→12 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refine analyze | Luzzati coordinate error obs: 0.24 Å | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→12 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 12 Å / σ(F): 0 / Rfactor obs: 0.1776 / Rfactor Rfree: 0.2109 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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