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Yorodumi- PDB-1byd: CRYSTAL STRUCTURES OF SOYBEAN BETA-AMYLASE REACTED WITH BETA-MALT... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1byd | |||||||||
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Title | CRYSTAL STRUCTURES OF SOYBEAN BETA-AMYLASE REACTED WITH BETA-MALTOSE AND MALTAL: ACTIVE SITE COMPONENTS AND THEIR APPARENT ROLE IN CATALYSIS | |||||||||
Components | BETA-AMYLASE | |||||||||
Keywords | HYDROLASE(O-GLYCOSYL) | |||||||||
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 / Resolution: 2.2 Å | |||||||||
Authors | Mikami, B. / Degano, M. / Hehre, E.J. / Sacchettini, J.C. | |||||||||
Citation | Journal: Biochemistry / Year: 1994 Title: Crystal structures of soybean beta-amylase reacted with beta-maltose and maltal: active site components and their apparent roles in catalysis. Authors: Mikami, B. / Degano, M. / Hehre, E.J. / Sacchettini, J.C. #1: Journal: Biochemistry / Year: 1993 Title: The 2.0-Angstroms Resolution Structure of Soybean Beta-Amylase Complexed with Alpha-Cyclodextrin Authors: Mikami, B. / Hehre, E.J. / Sato, M. / Katsube, Y. / Hirose, M. / Morita, Y. / Sacchettini, J.C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1byd.cif.gz | 118.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1byd.ent.gz | 89.9 KB | Display | PDB format |
PDBx/mmJSON format | 1byd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1byd_validation.pdf.gz | 511.6 KB | Display | wwPDB validaton report |
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Full document | 1byd_full_validation.pdf.gz | 536.2 KB | Display | |
Data in XML | 1byd_validation.xml.gz | 14.8 KB | Display | |
Data in CIF | 1byd_validation.cif.gz | 23.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/by/1byd ftp://data.pdbj.org/pub/pdb/validation_reports/by/1byd | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Atom site foot note | 1: LEU 419 - ARG 420 OMEGA = 12.15 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION |
-Components
#1: Protein | Mass: 56071.316 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Glycine max (soybean) / References: UniProt: P10538, beta-amylase | ||||||
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#2: Polysaccharide | #3: Chemical | ChemComp-SO4 / | #4: Water | ChemComp-HOH / | Nonpolymer details | THIS STRUCTURE CONTAINS TWO 2'-DEOXYMALTO | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.76 Å3/Da / Density % sol: 55.38 % | |||||||||||||||
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Crystal grow | *PLUS Method: unknown / Details: Morita, Y., (1975) J. Biochem., 77, 343. | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Num. obs: 46480 / Num. measured all: 176655 |
-Processing
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Refinement | Resolution: 2.2→9 Å / σ(F): 2 /
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Refinement step | Cycle: LAST / Resolution: 2.2→9 Å
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Refine LS restraints |
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