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Yorodumi- PDB-1jd9: CRYSTAL STRUCTURE ANALYSIS OF THE MUTANT K300Q OF PSEUDOALTEROMON... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1jd9 | ||||||
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Title | CRYSTAL STRUCTURE ANALYSIS OF THE MUTANT K300Q OF PSEUDOALTEROMONAS HALOPLANCTIS ALPHA-AMYLASE | ||||||
Components | ALPHA-AMYLASE | ||||||
Keywords | HYDROLASE / ALPHA-BETA BARREL / GLYCOSYL HYDROLASE / ALLOSTERIC ACTIVATION | ||||||
Function / homology | Function and homology information alpha-amylase / alpha-amylase activity / carbohydrate metabolic process / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | Pseudoalteromonas haloplanktis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.5 Å | ||||||
Authors | Aghajari, N. / Haser, R. | ||||||
Citation | Journal: PROTEIN SCI. / Year: 2002 Title: Structural basis of alpha-amylase activation by chloride Authors: Aghajari, N. / Feller, G. / Gerday, C. / Haser, R. #1: 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. #2: 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. / Haser, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jd9.cif.gz | 102.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jd9.ent.gz | 77.5 KB | Display | PDB format |
PDBx/mmJSON format | 1jd9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1jd9_validation.pdf.gz | 417.9 KB | Display | wwPDB validaton report |
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Full document | 1jd9_full_validation.pdf.gz | 423.4 KB | Display | |
Data in XML | 1jd9_validation.xml.gz | 19.3 KB | Display | |
Data in CIF | 1jd9_validation.cif.gz | 27.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jd/1jd9 ftp://data.pdbj.org/pub/pdb/validation_reports/jd/1jd9 | HTTPS FTP |
-Related structure data
Related structure data | 1jd7C 1l0pC 1aqhS S: Starting model for refinement C: citing same article (ref.) |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 49379.789 Da / Num. of mol.: 1 / Mutation: K300Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudoalteromonas haloplanktis (bacteria) Strain: A23 / Gene: AMY / Plasmid: PAH12WT / Gene (production host): HB101 / Production host: Escherichia coli (E. coli) / References: UniProt: P29957, alpha-amylase |
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#2: Chemical | ChemComp-CA / |
#3: Water | ChemComp-HOH / |
Has protein modification | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.89 Å3/Da / Density % sol: 57.44 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7 Details: MPD, Hepes, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 288 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 29, 1997 / 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: 2.5→43.03 Å / Num. all: 16759 / Num. obs: 16759 / % possible obs: 81.8 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 4 / Redundancy: 3.4 % / Biso Wilson estimate: 32.92 Å2 / Rmerge(I) obs: 0.216 / Net I/σ(I): 3 |
Reflection shell | Resolution: 2.5→2.64 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.564 / Num. unique all: 1146 / % possible all: 39.2 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 1AQH Resolution: 2.5→42.7 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.5→42.7 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.53 Å /
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