+Open data
-Basic information
Entry | Database: PDB / ID: 2dqx | ||||||
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Title | mutant beta-amylase (W55R) from soy bean | ||||||
Components | Beta-amylase | ||||||
Keywords | HYDROLASE / amylase mutant sliding soy bean | ||||||
Function / homology | Function and homology information beta-amylase / beta-amylase activity / amylopectin maltohydrolase activity / polysaccharide catabolic process Similarity search - Function | ||||||
Biological species | Glycine max (soybean) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Ishikawa, K. | ||||||
Citation | Journal: Biochemistry / Year: 2007 Title: Kinetic and structural analysis of enzyme sliding on a substrate: multiple attack in beta-amylase Authors: Ishikawa, K. / Nakatani, H. / Katsuya, Y. / Fukazawa, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2dqx.cif.gz | 115.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2dqx.ent.gz | 87.5 KB | Display | PDB format |
PDBx/mmJSON format | 2dqx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dq/2dqx ftp://data.pdbj.org/pub/pdb/validation_reports/dq/2dqx | HTTPS FTP |
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-Related structure data
Related structure data | 1wdpS 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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-Components
#1: Protein | Mass: 55970.172 Da / Num. of mol.: 1 / Mutation: W55R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Glycine max (soybean) / Plasmid: pBAMSO / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: Q42795, beta-amylase |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54.4 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.4 Details: 0.1M sodium acetate (pH 5.4), 1mM EDTA, 50% ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL24XU / Wavelength: 0.835 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 12, 1999 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.835 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→19.95 Å / Num. obs: 31087 / % possible obs: 98.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 5 Å2 / Rmerge(I) obs: 0.074 |
Reflection shell | Highest resolution: 2.2 Å / % possible all: 98 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1WDP Resolution: 2.2→19.9 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2526968.69 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 60.5074 Å2 / ksol: 0.406937 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 11.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→19.9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
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Xplor file |
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