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- PDB-1v08: Crystal structure of the Zea maze beta-glucosidase-1 in complex w... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1v08 | ||||||
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Title | Crystal structure of the Zea maze beta-glucosidase-1 in complex with gluco-tetrazole | ||||||
![]() | BETA-GLUCOSIDASE | ||||||
![]() | HYDROLASE / BETA-GLUCOSIDASE / GLYCOSIDE HYDROLASE / DIMBOA-GLUCOSIDE / INHIBITOR / PEST DEFENSE / FAMILY GH1 / CHLOROPLAST / TRANSIT PEPTIDE | ||||||
Function / homology | ![]() galactosidase activity / fucosidase activity / xylanase activity / 4-hydroxy-7-methoxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl glucoside beta-D-glucosidase / DIMBOA glucoside beta-D-glucosidase activity / cytokinin-activated signaling pathway / mannosidase activity / cellulose 1,4-beta-cellobiosidase activity / scopolin beta-glucosidase activity / beta-glucosidase ...galactosidase activity / fucosidase activity / xylanase activity / 4-hydroxy-7-methoxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl glucoside beta-D-glucosidase / DIMBOA glucoside beta-D-glucosidase activity / cytokinin-activated signaling pathway / mannosidase activity / cellulose 1,4-beta-cellobiosidase activity / scopolin beta-glucosidase activity / beta-glucosidase / beta-glucosidase activity / chloroplast / carbohydrate metabolic process Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Moriniere, J. / Verdoucq, L. / Bevan, D.R. / Esen, A. / Henrissat, B. / Czjzek, M. | ||||||
![]() | ![]() Title: Structural Determinants of Substrate Specificity in Family 1 Beta-Glucosidases: Novel Insights from the Crystal Structure of Sorghum Dhurrinase-1, a Plant Beta-Glucosidase with Strict ...Title: Structural Determinants of Substrate Specificity in Family 1 Beta-Glucosidases: Novel Insights from the Crystal Structure of Sorghum Dhurrinase-1, a Plant Beta-Glucosidase with Strict Specificity, in Complex with its Natural Substrate Authors: Verdoucq, L. / Moriniere, J. / Bevan, D.R. / Esen, A. / Vasella, A. / Henrissat, B. / Czjzek, M. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA BA" IN EACH CHAIN ON SHEET RECORDS ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-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 | ![]() | 224.6 KB | Display | ![]() |
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PDB format | ![]() | 180.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 460.8 KB | Display | ![]() |
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Full document | ![]() | 475 KB | Display | |
Data in XML | ![]() | 44.9 KB | Display | |
Data in CIF | ![]() | 67.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1v02C ![]() 1v03C ![]() 1e1eS 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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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.20717, -0.35231, -0.91267), Vector: |
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Components
#1: Protein | Mass: 58458.422 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-NTZ / #3: Water | ChemComp-HOH / | Compound details | ENGINEERED MUTATION IN CHAIN A AND B, GLU 245 TO ASP CATALYTIC ACTIVITY: HYDROLYSIS OF TERMINAL, ...ENGINEERED | Sequence details | ASP A 191, SITE DIRECTED MUTATION | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.89 Å3/Da / Density % sol: 57.5 % |
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Crystal grow | pH: 7.5 / Details: 22% PEG 4000, 5% ISOPROPANOL, 0.1 M HEPES PH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Date: Feb 15, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→29.8 Å / Num. obs: 92037 / % possible obs: 96.6 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 6.9 |
Reflection shell | Resolution: 1.95→2.01 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.456 / Mean I/σ(I) obs: 1.5 / % possible all: 94 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1E1E Resolution: 1.9→29.75 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.949 / SU B: 2.826 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.138 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.38 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→29.75 Å
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