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Yorodumi- PDB-1jd7: CRYSTAL STRUCTURE ANALYSIS OF THE MUTANT K300R OF PSEUDOALTEROMON... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1jd7 | ||||||
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Title | CRYSTAL STRUCTURE ANALYSIS OF THE MUTANT K300R 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 space / metal ion binding Similarity search - Function | ||||||
Biological species | Pseudoalteromonas haloplanktis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.25 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 | 1jd7.cif.gz | 108.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jd7.ent.gz | 81.1 KB | Display | PDB format |
PDBx/mmJSON format | 1jd7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1jd7_validation.pdf.gz | 412.2 KB | Display | wwPDB validaton report |
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Full document | 1jd7_full_validation.pdf.gz | 416.3 KB | Display | |
Data in XML | 1jd7_validation.xml.gz | 21.4 KB | Display | |
Data in CIF | 1jd7_validation.cif.gz | 32.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jd/1jd7 ftp://data.pdbj.org/pub/pdb/validation_reports/jd/1jd7 | HTTPS FTP |
-Related structure data
Related structure data | 1jd9C 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
#1: Protein | Mass: 49408.855 Da / Num. of mol.: 1 / Mutation: K300R 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: Chemical | #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: 2.75 Å3/Da / Density % sol: 55.32 % |
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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: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 16, 2001 / Details: mirrors |
Radiation | Monochromator: OSMIC MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→25.7 Å / Num. all: 25155 / Num. obs: 25136 / % possible obs: 95.8 % / Observed criterion σ(F): 5 / Observed criterion σ(I): 5 / Redundancy: 3 % / Rmerge(I) obs: 0.133 / Net I/σ(I): 3.1 |
Reflection shell | Resolution: 2.25→2.3 Å / Redundancy: 2 % / Rmerge(I) obs: 0.572 / % possible all: 53.9 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 1AQH Resolution: 2.25→25.7 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: 2.25→25.7 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.25→2.27 Å /
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