+Open data
-Basic information
Entry | Database: PDB / ID: 1ud6 | ||||||
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Title | Crystal structure of AmyK38 with potassium ion | ||||||
Components | amylase | ||||||
Keywords | HYDROLASE / calcium-free / alkaline / alpha-amylase | ||||||
Function / homology | Function and homology information alpha-amylase activity / carbohydrate metabolic process / calcium ion binding / extracellular space Similarity search - Function | ||||||
Biological species | Bacillus sp. KSM-K38 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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 | 1ud6.cif.gz | 113.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ud6.ent.gz | 86.8 KB | Display | PDB format |
PDBx/mmJSON format | 1ud6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ud6_validation.pdf.gz | 364.8 KB | Display | wwPDB validaton report |
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Full document | 1ud6_full_validation.pdf.gz | 369.1 KB | Display | |
Data in XML | 1ud6_validation.xml.gz | 10.8 KB | Display | |
Data in CIF | 1ud6_validation.cif.gz | 17 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ud/1ud6 ftp://data.pdbj.org/pub/pdb/validation_reports/ud/1ud6 | HTTPS FTP |
-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: 55145.668 Da / Num. of mol.: 1 / Fragment: residues 1-480 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 | ChemComp-K / #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: 3.52 Å3/Da / Density % sol: 65.02 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: soaking of native crystals / pH: 6.8 Details: PEG 8000, potassium acetate, glycerol, MES-KOH, Tris-HCl, pH 6.8, Soaking of native crystals, 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: BL44B2 / Wavelength: 1 Å |
Detector | Type: MARRESEARCH / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→100 Å / Num. all: 27104 / Num. obs: 27104 / % possible obs: 100 % / Redundancy: 15.6 % / Biso Wilson estimate: 27.9 Å2 / Rmerge(I) obs: 0.099 / Net I/σ(I): 30.8 |
Reflection shell | Resolution: 2.5→2.59 Å / Rmerge(I) obs: 0.272 / Mean I/σ(I) obs: 12.9 / Num. unique all: 2636 / % possible all: 100 |
Reflection | *PLUS Num. obs: 25846 / % possible obs: 95.4 % / Num. measured all: 404246 |
Reflection shell | *PLUS % possible obs: 89.9 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Model of native AmyK38 structure Resolution: 2.5→44.18 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 2493117.02 / 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: 34.3356 Å2 / ksol: 0.378991 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→44.18 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.02 / 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: 0.251 / Rfactor Rwork: 0.215 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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