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Yorodumi- PDB-1tmq: STRUCTURE OF TENEBRIO MOLITOR LARVAL ALPHA-AMYLASE IN COMPLEX WIT... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1tmq | |||||||||
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Title | STRUCTURE OF TENEBRIO MOLITOR LARVAL ALPHA-AMYLASE IN COMPLEX WITH RAGI BIFUNCTIONAL INHIBITOR | |||||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / ALPHA-AMYLASE / CARBOHYDRATE METABOLISM / ALPHA-1 / 4-GLUCAN-4-GLUCANOHYDROLASE / HYDROLASE BIFUNCTIONAL ALPHA-AMYLASE/TRYPSIN INHIBITOR / COMPLEX (ENZYME- INHIBITOR) / HYDROLASE-HYDROLASE INHIBITOR COMPLEX | |||||||||
Function / homology | Function and homology information alpha-amylase inhibitor activity / alpha-amylase / carbohydrate catabolic process / alpha-amylase activity / chloride ion binding / serine-type endopeptidase inhibitor activity / calcium ion binding / extracellular region Similarity search - Function | |||||||||
Biological species | Tenebrio molitor (yellow mealworm) Eleusine coracana (finger millet) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | |||||||||
Authors | Gomis-Rueth, F.X. / Strobl, S. / Glockshuber, R. | |||||||||
Citation | Journal: Structure / Year: 1998 Title: A novel strategy for inhibition of alpha-amylases: yellow meal worm alpha-amylase in complex with the Ragi bifunctional inhibitor at 2.5 A resolution. Authors: Strobl, S. / Maskos, K. / Wiegand, G. / Huber, R. / Gomis-Ruth, F.X. / Glockshuber, R. #1: Journal: FEBS Lett. / Year: 1997 Title: The Alpha-Amylase from the Yellow Meal Worm: Complete Primary Structure, Crystallization and Preliminary X-Ray Analysis Authors: Strobl, S. / Gomis-Ruth, F.X. / Maskos, K. / Frank, G. / Huber, R. / Glockshuber, R. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1tmq.cif.gz | 132.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1tmq.ent.gz | 101.6 KB | Display | PDB format |
PDBx/mmJSON format | 1tmq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1tmq_validation.pdf.gz | 377.1 KB | Display | wwPDB validaton report |
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Full document | 1tmq_full_validation.pdf.gz | 385.8 KB | Display | |
Data in XML | 1tmq_validation.xml.gz | 13.4 KB | Display | |
Data in CIF | 1tmq_validation.cif.gz | 22 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tm/1tmq ftp://data.pdbj.org/pub/pdb/validation_reports/tm/1tmq | HTTPS FTP |
-Related structure data
Related structure data | 1bipS 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: 51263.066 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tenebrio molitor (yellow mealworm) / Tissue: LARVAE / References: UniProt: P56634, alpha-amylase |
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#2: Protein | Mass: 12715.823 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Eleusine coracana (finger millet) / Organ: SEED / References: UniProt: P01087 |
#3: Chemical | ChemComp-CL / |
#4: Chemical | ChemComp-CA / |
#5: Water | ChemComp-HOH / |
Compound details | THE ALPHA-AMYLASE N-TERMINUS BLOCKS AGAINST AMINOPEPTIDASE ACTIVITY BY GLUTAMINE CYCLIZATION TO ...THE ALPHA-AMYLASE N-TERMINUS BLOCKS AGAINST AMINOPEPTI |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.22 Å3/Da / Density % sol: 61.83 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Details: 200MM AMMONIUM PHOSPHATE, 100MM TRIS-HCL, PH 8.5, 50% (W/V) 2-METHYL-2,4- PENTANEDIOL | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 5.4 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
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Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Monochromator: GRAPHITE CRYSTAL / 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→20 Å / Num. obs: 28178 / % possible obs: 97.3 % / Observed criterion σ(I): 3 / Redundancy: 2.8 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 5.5 |
Reflection shell | Resolution: 2.5→2.56 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.284 / Mean I/σ(I) obs: 2.5 / % possible all: 89.8 |
Reflection | *PLUS Observed criterion σ(I): 3 / Num. measured all: 78106 |
Reflection shell | *PLUS % possible obs: 89.8 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1BIP Resolution: 2.5→7 Å / Cross valid method: FREE R FACTOR / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 2.5→7 Å
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 7 Å / σ(F): 0 / % reflection Rfree: 7 % | ||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||
Refine LS restraints | *PLUS
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