+Open data
-Basic information
Entry | Database: PDB / ID: 1ud3 | ||||||
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Title | Crystal structure of AmyK38 N289H mutant | ||||||
Components | amylase | ||||||
Keywords | HYDROLASE / calcium-free / alkaline / alpha-amylase | ||||||
Function / homology | Function and homology information hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process / calcium ion binding / extracellular region Similarity search - Function | ||||||
Biological species | Bacillus sp. KSM-K38 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | ||||||
Authors | Nonaka, T. / Fujihashi, M. / Kita, A. / Hagihara, H. / Ozaki, K. / Ito, S. / Miki, K. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2003 Title: Crystal structure of calcium-free alpha-amylase from Bacillus sp. strain KSM-K38 (AmyK38) and its sodium ion binding sites Authors: Nonaka, T. / Fujihashi, M. / Kita, A. / Hagihara, H. / Ozaki, K. / Ito, S. / Miki, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ud3.cif.gz | 113.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ud3.ent.gz | 87.1 KB | Display | PDB format |
PDBx/mmJSON format | 1ud3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ud/1ud3 ftp://data.pdbj.org/pub/pdb/validation_reports/ud/1ud3 | HTTPS FTP |
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-Related 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: 55169.711 Da / Num. of mol.: 1 / Fragment: residues 1-480 / Mutation: N289H Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus sp. KSM-K38 (bacteria) / Plasmid: pHSP64 / Production host: Bacillus subtilis (bacteria) / References: UniProt: Q93I48, alpha-amylase | ||
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#2: Chemical | #3: 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: 3.51 Å3/Da / Density % sol: 64.96 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: MPD, PEG 4000, sodium citrate, Tris-HCl, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 293 K / pH: 7.5 / 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: SYNCHROTRON / Site: SPring-8 / Beamline: BL45PX / Wavelength: 1.02 Å |
Detector | Detector: CCD |
Radiation | Monochromator: Diamond (4 0 0) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.02 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→100 Å / Num. all: 42227 / Num. obs: 42227 / % possible obs: 99.9 % / Redundancy: 8.5 % / Biso Wilson estimate: 23.2 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 19.5 |
Reflection shell | Resolution: 2.15→2.19 Å / Rmerge(I) obs: 0.296 / Mean I/σ(I) obs: 3.4 / Num. unique all: 2073 / % possible all: 99.9 |
Reflection | *PLUS Num. obs: 40862 / % possible obs: 96.7 % / Num. measured all: 345465 |
Reflection shell | *PLUS % possible obs: 91 % / Mean I/σ(I) obs: 3.42 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Model of AmyK38 wild-type structure Resolution: 2.15→76.48 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2806978.15 / Data cutoff low absF: 0 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 56.1236 Å2 / ksol: 0.359969 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.15→76.48 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.15→2.28 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Lowest resolution: 100 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.264 / Rfactor Rwork: 0.234 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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