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Yorodumi- PDB-7upv: Structure of maize BZR1-type beta-amylase provides new insights i... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7upv | ||||||
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Title | Structure of maize BZR1-type beta-amylase provides new insights into its noncatalytic adaptation | ||||||
Components | Beta-amylase | ||||||
Keywords | HYDROLASE / GH-14 / maize beta-amylase / BZR1-BAM8 | ||||||
Function / homology | Function and homology information beta-amylase / beta-amylase activity / amylopectin maltohydrolase activity / polysaccharide catabolic process / regulation of gene expression Similarity search - Function | ||||||
Biological species | Zea mays (maize) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å | ||||||
Authors | Palayam, M. / Sun, F. / Shabek, N. | ||||||
Funding support | United States, 1items
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Citation | Journal: J.Struct.Biol. / Year: 2022 Title: Structure of maize BZR1-type beta-amylase BAM8 provides new insights into its noncatalytic adaptation. Authors: Sun, F. / Palayam, M. / Shabek, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7upv.cif.gz | 103.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7upv.ent.gz | 75.4 KB | Display | PDB format |
PDBx/mmJSON format | 7upv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7upv_validation.pdf.gz | 441.3 KB | Display | wwPDB validaton report |
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Full document | 7upv_full_validation.pdf.gz | 445.8 KB | Display | |
Data in XML | 7upv_validation.xml.gz | 17.5 KB | Display | |
Data in CIF | 7upv_validation.cif.gz | 23.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/up/7upv ftp://data.pdbj.org/pub/pdb/validation_reports/up/7upv | HTTPS FTP |
-Related structure data
Related structure data | 1byaS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 51447.871 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Zea mays (maize) / Gene: ZEAMMB73_Zm00001d053975 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1D6QTZ9, beta-amylase |
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#2: Chemical | ChemComp-GOL / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 38.93 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 0.2M MgCl2, 0.1M Sodium citrate tribasic dihydrate, 8% Polyethylene glycol 20000 PH range: 5-6 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 12, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 35028 / % possible obs: 98.19 % / Redundancy: 3.2 % / Rsym value: 0.05 / Net I/σ(I): 14.7 |
Reflection shell | Resolution: 1.8→1.9 Å / Num. unique obs: 3198 / CC1/2: 0.187 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1BYA Resolution: 1.84→44.83 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.93 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 95.34 Å2 / Biso mean: 27.1083 Å2 / Biso min: 12.1 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.84→44.83 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
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