+Open data
-Basic information
Entry | Database: PDB / ID: 1b0i | ||||||
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Title | ALPHA-AMYLASE FROM ALTEROMONAS HALOPLANCTIS | ||||||
Components | PROTEIN (ALPHA-AMYLASE) | ||||||
Keywords | HYDROLASE / ALPHA-AMYLASE / ALPHA-1 / 4-GLUCAN-4-GLUCANOHYDROLASE / BETA-ALPHA-EIGHT BARREL / PSYCHROPHILIC ENZYME | ||||||
Function / homology | Function and homology information alpha-amylase / alpha-amylase activity / carbohydrate metabolic process / extracellular space / metal ion binding Similarity search - Function | ||||||
Biological species | Pseudoalteromonas haloplanktis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Aghajari, N. / Haser, R. | ||||||
Citation | Journal: Structure / Year: 1998 Title: Structures of the psychrophilic Alteromonas haloplanctis alpha-amylase give insights into cold adaptation at a molecular level. Authors: Aghajari, N. / Feller, G. / Gerday, C. / Haser, R. #1: Journal: Protein Sci. / Year: 1998 Title: Crystal Structures of the Psychrophilic Alpha-amylase from Alteromonas Haloplanctis in Its Native Form and Complexed with an Inhibitor Authors: Aghajari, N. / Feller, G. / Gerday, C.H. / Haser, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1b0i.cif.gz | 119.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1b0i.ent.gz | 91.2 KB | Display | PDB format |
PDBx/mmJSON format | 1b0i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1b0i_validation.pdf.gz | 412 KB | Display | wwPDB validaton report |
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Full document | 1b0i_full_validation.pdf.gz | 413.3 KB | Display | |
Data in XML | 1b0i_validation.xml.gz | 17.5 KB | Display | |
Data in CIF | 1b0i_validation.cif.gz | 24.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b0/1b0i ftp://data.pdbj.org/pub/pdb/validation_reports/b0/1b0i | HTTPS FTP |
-Related structure data
Related structure data | 1aqhS S: Starting model for refinement |
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Similar 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: 49380.840 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudoalteromonas haloplanktis (bacteria) Strain: ALTEROMONAS HALOPLANCTIS A23 / Gene: AMY / Production host: Escherichia coli (E. coli) / References: UniProt: P29957, alpha-amylase |
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#2: Chemical | ChemComp-CA / |
#3: Chemical | ChemComp-CL / |
#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: 2.78 Å3/Da / Density % sol: 56 % | ||||||||||||||||||||
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Crystal grow | pH: 7 / Details: pH 7.0 | ||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 288 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Details: COLLIMATOR |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→48 Å / Num. obs: 21666 / % possible obs: 98 % / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Rsym value: 0.177 / Net I/σ(I): 4 |
Reflection shell | Resolution: 2.4→2.53 Å / Redundancy: 5.8 % / Mean I/σ(I) obs: 1.1 / Rsym value: 0.682 / % possible all: 95.8 |
Reflection | *PLUS Num. measured all: 128066 / Rmerge(I) obs: 0.177 |
Reflection shell | *PLUS % possible obs: 95.8 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: WILDTYPE AHA (1AQH) Resolution: 2.4→20 Å / Rfactor Rfree error: 0.0046 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 0 Details: BULK SOLVENT REFINEMENT HAS BEEN APPLIED THROUGHOUT THE REFINEMENT PROCESS
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Refinement step | Cycle: LAST / Resolution: 2.4→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.53 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.843 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 20 Å / σ(F): 0 / Rfactor obs: 0.18 / Rfactor Rwork: 0.18 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.316 / Rfactor Rwork: 0.274 |