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Yorodumi- PDB-1e4n: Crystal structure of the inactive mutant Monocot (Maize ZMGlu1) b... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1e4n | ||||||
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Title | Crystal structure of the inactive mutant Monocot (Maize ZMGlu1) beta-glucosidase ZMGluE191D in complex with the natural aglycone DIMBOA | ||||||
Components | BETA-GLUCOSIDASE | ||||||
Keywords | HYDROLASE / GLYCOSIDE HYDROLASE / BETA-GLUCOSIDASE / FAMILY 1 / RETENTION OF THE ANOMERIC CONFIGURATION / INACTIVE MUTANT E191D / HYDROLASE COMPLEX WITH DIMBOA | ||||||
Function / homology | Function and homology information 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 | ZEA MAYS (maize) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Czjzek, M. / Cicek, M. / Bevan, D.R. / Zamboni, V. / Henrissat, B. / Esen, A. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2000 Title: The Mechanism of Substrate (Aglycone) Specificity in Beta -Glucosidases is Revealed by Crystal Structures of Mutant Maize Beta -Glucosidase-Dimboa, -Dimboaglc, and -Dhurrin Complexes Authors: Czjzek, M. / Cicek, M. / Zamboni, V. / Bevan, D.R. / Henrissat, B. / Esen, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1e4n.cif.gz | 212.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1e4n.ent.gz | 170.2 KB | Display | PDB format |
PDBx/mmJSON format | 1e4n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1e4n_validation.pdf.gz | 448.7 KB | Display | wwPDB validaton report |
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Full document | 1e4n_full_validation.pdf.gz | 470.6 KB | Display | |
Data in XML | 1e4n_validation.xml.gz | 42.3 KB | Display | |
Data in CIF | 1e4n_validation.cif.gz | 60 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e4/1e4n ftp://data.pdbj.org/pub/pdb/validation_reports/e4/1e4n | HTTPS FTP |
-Related structure data
Related structure data | 1e4lC 1e55C 1e56C 1e1eS S: Starting model for refinement 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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.82128, 0.36548, -0.43809), Vector: |
-Components
#1: Protein | Mass: 58458.422 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ZEA MAYS (maize) / Strain: CV. MUTIN / Tissue: COLEOPTILE / Organelle: CHLOROPLAST / Plasmid: PET-21A / Gene (production host): GLU1 / Production host: ESCHERICHIA COLI (E. coli) / Variant (production host): PLYS S / References: UniProt: P49235, beta-glucosidase #2: Chemical | #3: Water | ChemComp-HOH / | Compound details | CHAIN A, B ENGINEERED | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.43 % | ||||||||||||||||||||
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Crystal grow | pH: 7.5 / Details: 22 % PEG 4000, 5 % ISOPROPANOL, 0.1 M HEPES PH 7.5 | ||||||||||||||||||||
Crystal grow | *PLUS 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: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.93 |
Detector | Date: Mar 15, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.93 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→29.1 Å / Num. obs: 58526 / % possible obs: 96.7 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.083 / Rsym value: 0.068 / Net I/σ(I): 7.7 |
Reflection shell | Resolution: 2.1→2.21 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.484 / Mean I/σ(I) obs: 1.3 / Rsym value: 0.386 / % possible all: 90.3 |
Reflection shell | *PLUS % possible obs: 90.3 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1E1E Resolution: 2.1→29 Å / Data cutoff high absF: 1000000 / Cross valid method: THROUGHOUT / σ(F): 0.1 Details: THE N- AND C-TERMINAL RESIDUES WERE NOT SEEN IN THE ELECTRON DENSITY MAPS
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 43.15 Å2 / ksol: 0.3556 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.37 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→29 Å
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Refine LS restraints |
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Refine LS restraints NCS | Rms dev position: 0.306 Å / Weight position: 5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.1→2.18 Å / Total num. of bins used: 10
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.266 / Rfactor Rwork: 0.218 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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