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Yorodumi- PDB-1e1f: Crystal structure of a Monocot (Maize ZMGlu1) beta-glucosidase in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1e1f | ||||||
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Title | Crystal structure of a Monocot (Maize ZMGlu1) beta-glucosidase in complex with p-Nitrophenyl-beta-D-thioglucoside | ||||||
Components | BETA-GLUCOSIDASE | ||||||
Keywords | HYDROLASE / GLYCOSIDE HYDROLASE / BETA-GLUCOSIDASE / FAMILY 1 / RETENTION OF THE ANOMERIC CONFIGURATION / PNP-BETA-D-THIOGLUCOSIDE | ||||||
Function / homology | Function and homology information fucosidase activity / xylanase activity / galactosidase 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 activity ...fucosidase activity / xylanase activity / galactosidase 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 activity / beta-glucosidase / chloroplast / carbohydrate metabolic process Similarity search - Function | ||||||
Biological species | ZEA MAYS (maize) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Czjzek, M. / Cicek, M. / Bevan, D.R. / Henrissat, B. / Esen, A. | ||||||
Citation | Journal: Biochem.J. / Year: 2001 Title: Crystal Structure of a Monocotyledon (Maize Zmglu1) Beta-Glucosidase and a Model of its Complex with P-Nitrophenyl Beta-D-Thioglucoside Authors: Czjzek, M. / Cicek, M. / Zamboni, V. / Burmeister, W.P. / Bevan, D.R. / Henrissat, B. / Esen, A. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" 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. THE SHEETS PRESENTED AS "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. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1e1f.cif.gz | 210.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1e1f.ent.gz | 169.2 KB | Display | PDB format |
PDBx/mmJSON format | 1e1f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e1/1e1f ftp://data.pdbj.org/pub/pdb/validation_reports/e1/1e1f | HTTPS FTP |
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-Related structure data
Related structure data | 1e1eC 1cbgS 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: (0.97447, -0.16779, -0.14917), Vector: |
-Components
#1: Protein | Mass: 58472.445 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ZEA MAYS (maize) / Strain: CV. MUTIN / Tissue: COLEOPTILE / Organelle: CHLOROPLAST / Plasmid: PET-21A / Cell (production host): PLYS S CELLS / Gene (production host): GLU1 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P49235, beta-glucosidase #2: Sugar | #3: Water | ChemComp-HOH / | Compound details | THE INHIBITOR IN THE ACTIVE SITE IS DISORDERED AND PROBABLY PRESENT IN MORE THAN THE TWO DEPOSITED ...THE INHIBITOR IN THE ACTIVE SITE IS DISORDERED | |
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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: 2.57 Å3/Da / Density % sol: 52.05 % | ||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 5.6 Details: 27 % PEG 4000, 1.5 % 1,2,3-HEPTANETRIOL 0.2 M AMMONIUM ACETATE, 0.1 M SODIUM CITRATE PH 5.6 | ||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7 / 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: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 |
Detector | Date: Mar 15, 1999 |
Radiation | Monochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→40 Å / Num. obs: 340923 / % possible obs: 99 % / Redundancy: 3.1 % / Rsym value: 0.094 / Net I/σ(I): 4.2 |
Reflection shell | Resolution: 2.59→2.65 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 2 / Rsym value: 0.263 / % possible all: 97.5 |
Reflection | *PLUS Num. obs: 34732 / % possible obs: 99.8 % / Num. measured all: 137688 / Rmerge(I) obs: 0.094 |
Reflection shell | *PLUS % possible obs: 97.5 % / Rmerge(I) obs: 0.263 / Mean I/σ(I) obs: 1.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1CBG Resolution: 2.6→39 Å / Data cutoff high absF: 10000000 / Cross valid method: THROUGHOUT / σ(F): 0.1
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 18.93 Å2 / ksol: 0.2966 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.03 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.6→39 Å
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Refine LS restraints |
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Refine LS restraints NCS | Rms dev position: 0.395 Å / Weight position: 10 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.6→2.69 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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