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Yorodumi- PDB-1l0p: CRYSTAL STRUCTURE ANALYSIS OF THE COMPLEX BETWEEN PSYCHROPHILIC A... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1l0p | ||||||
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Title | CRYSTAL STRUCTURE ANALYSIS OF THE COMPLEX BETWEEN PSYCHROPHILIC ALPHA AMYLASE FROM PSEUDOALTEROMONAS HALOPLANCTIS AND NITRATE | ||||||
Components | ALPHA-AMYLASE | ||||||
Keywords | HYDROLASE / BETA-ALPHA-8-BARREL / 3 DOMAIN STRUCTURE | ||||||
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: 2.1 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1l0p.cif.gz | 102.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1l0p.ent.gz | 77.2 KB | Display | PDB format |
PDBx/mmJSON format | 1l0p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l0/1l0p ftp://data.pdbj.org/pub/pdb/validation_reports/l0/1l0p | HTTPS FTP |
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-Related structure data
Related structure data | 1jd7C 1jd9C 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: 48947.426 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudoalteromonas haloplanktis (bacteria) / References: UniProt: P29957, alpha-amylase |
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#2: Chemical | ChemComp-CA / |
#3: Chemical | ChemComp-NO3 / |
#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: 2.89 Å3/Da / Density % sol: 57.51 % | |||||||||||||||
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7 Details: MPD, Hepes, pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 292K | |||||||||||||||
Crystal grow | *PLUS pH: 7 / Details: Aghajari, N., (1996) Protein Sci., 5, 2128. | |||||||||||||||
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: ENRAF-NONIUS FR591 / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 28, 1998 |
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: 2.1→42.6 Å / Num. all: 29937 / Num. obs: 29641 / % possible obs: 89.3 % / Observed criterion σ(I): 1 / Redundancy: 5 % / Biso Wilson estimate: 21.7 Å2 / Rmerge(I) obs: 0.15 |
Reflection shell | Resolution: 2.1→2.21 Å / Redundancy: 4.5 % / % possible all: 90.5 |
Reflection | *PLUS Num. measured all: 149687 / Rmerge(I) obs: 0.15 |
Reflection shell | *PLUS % possible obs: 90.5 % |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 1AQH Resolution: 2.1→42.56 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: FINAL CYCLE OF REFINEMENT WAS CARRIED OUT USING CNS.
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Refinement step | Cycle: LAST / Resolution: 2.1→42.56 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 2.1 Å / Num. reflection obs: 29641 | |||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||
Displacement parameters | *PLUS |