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Yorodumi- PDB-1mwo: Crystal Structure Analysis of the Hyperthermostable Pyrocoocus wo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1mwo | ||||||
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Title | Crystal Structure Analysis of the Hyperthermostable Pyrocoocus woesei alpha-amylase | ||||||
Components | alpha amylase | ||||||
Keywords | HYDROLASE / (beta/alpha)8-barrel / alpha-amylase | ||||||
Function / homology | Function and homology information alpha-amylase / alpha-amylase activity / carbohydrate metabolic process / calcium ion binding / extracellular space Similarity search - Function | ||||||
Biological species | Pyrococcus woesei (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.2 Å | ||||||
Authors | Linden, A. / Mayans, O. / Meyer-Klaucke, W. / Antranikian, G. / Wilmanns, M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2003 Title: Differential Regulation of a Hyperthermophilic alpha-Amylase with a Novel (Ca,Zn) Two-metal Center by Zinc Authors: Linden, A. / Mayans, O. / Meyer-Klaucke, W. / Antranikian, G. / Wilmanns, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1mwo.cif.gz | 105.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mwo.ent.gz | 85.6 KB | Display | PDB format |
PDBx/mmJSON format | 1mwo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mw/1mwo ftp://data.pdbj.org/pub/pdb/validation_reports/mw/1mwo | 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: 50228.676 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus woesei (archaea) / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Bl21(DE3) References: UniProt: O08452, UniProt: Q7LYT7*PLUS, alpha-amylase | ||||
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#2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-CA / | #4: 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: 2.6 Å3/Da / Density % sol: 52.7 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG-MME 550, zinc sulfate, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 19 ℃ / 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: EMBL/DESY, Hamburg / Beamline: X11 / Wavelength: 0.91 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jul 23, 2000 |
Radiation | Monochromator: Triangular / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→20 Å / Num. all: 26004 / Num. obs: 26004 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 27.1 Å2 / Rsym value: 0.06 / Net I/σ(I): 10.2 |
Reflection shell | Highest resolution: 2.2 Å / Mean I/σ(I) obs: 3 / Num. unique all: 26004 / Rsym value: 0.178 / % possible all: 93.1 |
Reflection | *PLUS Highest resolution: 2.2 Å / Rmerge(I) obs: 0.06 |
Reflection shell | *PLUS Highest resolution: 2.22 Å / Lowest resolution: 2.28 Å / % possible obs: 93.1 % / Rmerge(I) obs: 0.178 |
-Processing
Software |
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Refinement | Method to determine structure: SIRAS / Resolution: 2.2→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 26.4 Å2
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Refine analyze | Luzzati coordinate error obs: 0.263 Å | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→20 Å
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Refine LS restraints |
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Xplor file |
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Refinement | *PLUS Rfactor Rwork: 0.19 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS |