+Open data
-Basic information
Entry | Database: PDB / ID: 1hxj | ||||||
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Title | CRYSTAL STRUCTURE OF THE MAIZE ZM-P60.1 BETA-GLUCOSIDASE | ||||||
Components | BETA-GLUCOSIDASE | ||||||
Keywords | HYDROLASE / GLYCOSIDE HYDROLASE / BETA-GLUCOSIDASE / FAMILY 1 / RETENTION OF THE ANOMERIC CONFIGURATION | ||||||
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: 2.05 Å | ||||||
Authors | Vevodova, J. / Su, X.-D. / Marek, J. / Brzobohaty, B. | ||||||
Citation | Journal: Plant Physiol. / Year: 2001 Title: Insights into the functional architecture of the catalytic center of a maize beta-glucosidase Zm-p60.1 Authors: Zouhar, J. / Vevodova, J. / Marek, J. / Damborsky, J. / Su, X.-D. / Brzobohaty, B. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2001 Title: Purification, Crystallization and Preliminary X-Ray Analysis of a Maize Cytokinin-Glucoside-Specific Beta-Glucosidase Authors: Vevodova, J. / Marek, J. / Zouhar, J. / Brzobohaty, B. / Su, X.-D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1hxj.cif.gz | 223.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1hxj.ent.gz | 178.9 KB | Display | PDB format |
PDBx/mmJSON format | 1hxj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1hxj_validation.pdf.gz | 434.1 KB | Display | wwPDB validaton report |
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Full document | 1hxj_full_validation.pdf.gz | 448.5 KB | Display | |
Data in XML | 1hxj_validation.xml.gz | 45.1 KB | Display | |
Data in CIF | 1hxj_validation.cif.gz | 67.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hx/1hxj ftp://data.pdbj.org/pub/pdb/validation_reports/hx/1hxj | HTTPS FTP |
-Related structure data
Related structure data | 1cbgS S: Starting model for refinement |
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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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Details | The second part of the biological assembly is generated by the two fold axis parallel to the a-axis |
-Components
#1: Protein | Mass: 58000.918 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: PRSET A / Gene (production host): ZM-P60.1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) PLYSS CELLS / References: UniProt: P49235, beta-glucosidase #2: Water | ChemComp-HOH / | |
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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: 1.89 Å3/Da / Density % sol: 35 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 20% PEG 4000, 0.1 M citrate buffer pH 5.6, 0.2 M ammonium acetate, VAPOR DIFFUSION, HANGING DROP at 294K | ||||||||||||||||||||||||
Crystal grow | *PLUS Method: unknown / PH range low: 5.9 / PH range high: 5.3 | ||||||||||||||||||||||||
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: MAX II / Beamline: I711 / Wavelength: 0.9831 / Wavelength: 0.9831 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 26, 2000 |
Radiation | Monochromator: monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9831 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→68 Å / Num. all: 52651 / Num. obs: 52651 / % possible obs: 94.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.7 % / Biso Wilson estimate: 7.6 Å2 / Rmerge(I) obs: 0.058 / Rsym value: 0.048 / Net I/σ(I): 15.5 |
Reflection shell | Resolution: 2.05→2.12 Å / Redundancy: 8.8 % / Rmerge(I) obs: 0.198 / Mean I/σ(I) obs: 4.9 / Num. unique all: 4711 / Rsym value: 0.174 / % possible all: 85.7 |
Reflection | *PLUS Lowest resolution: 68 Å / % possible obs: 94.7 % / Rmerge(I) obs: 0.053 |
Reflection shell | *PLUS Lowest resolution: 2.18 Å / % possible obs: 85.7 % / Rmerge(I) obs: 0.176 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1CBG Resolution: 2.05→34.93 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 983707.72 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 57.35 Å2 / ksol: 0.371 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.05→34.93 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.05→2.18 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Lowest resolution: 68 Å / Rfactor Rfree: 0.23 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rwork: 0.2 |