+Open data
-Basic information
Entry | Database: PDB / ID: 1ud8 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of AmyK38 with lithium ion | ||||||
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: 2.88 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1ud8.cif.gz | 110.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1ud8.ent.gz | 85.7 KB | Display | PDB format |
PDBx/mmJSON format | 1ud8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ud/1ud8 ftp://data.pdbj.org/pub/pdb/validation_reports/ud/1ud8 | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-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 | ||
---|---|---|---|
#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.52 Å3/Da / Density % sol: 65.04 % | ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 293 K / Method: soaking of native crystals / pH: 6.7 Details: PEG 8000, lithium acetate, glycerol, MES-LiOH, Tris-HCl, pH 6.7, 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
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
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: 2.88→100 Å / Num. all: 17867 / Num. obs: 17867 / % possible obs: 100 % / Redundancy: 21.1 % / Biso Wilson estimate: 54.8 Å2 / Rmerge(I) obs: 0.137 / Net I/σ(I): 23.5 |
Reflection shell | Resolution: 2.88→2.98 Å / Rmerge(I) obs: 0.297 / Mean I/σ(I) obs: 12.8 / Num. unique all: 1739 / % possible all: 100 |
Reflection | *PLUS Num. obs: 17227 / % possible obs: 96.4 % / Num. measured all: 363444 |
Reflection shell | *PLUS % possible obs: 90.3 % |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Model of native AmyK38 structure Resolution: 2.88→59.28 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 2038246.49 / Data cutoff low absF: 0 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: This structure was determined from the dataset of the crystal soaked into Li+ ion containing solution. However, metal atoms were refined as sodium ions.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 38.4544 Å2 / ksol: 0.411481 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.2 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.88→59.28 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.88→3.06 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 100 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.265 / Rfactor Rwork: 0.21 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|