+Open data
-Basic information
Entry | Database: PDB / ID: 1aqm | ||||||
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Title | ALPHA-AMYLASE FROM ALTEROMONAS HALOPLANCTIS COMPLEXED WITH TRIS | ||||||
Components | ALPHA-AMYLASE | ||||||
Keywords | HYDROLASE / ALPHA-AMYLASE / ALPHA-1 / 4-GLUCAN-4-GLUCANOHYDROLASE / BETA-ALPHA-EIGHT BARREL / PSYCHROPHILIC ENZYME / GLYCOSIDASE INHIBITION | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Aghajari, N. / Haser, R. | ||||||
Citation | 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. #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: 1996 Title: Crystallization and Preliminary X-Ray Diffraction Studies of Alpha-Amylase from the Antarctic Psychrophile Alteromonas Haloplanctis A23 Authors: Aghajari, N. / Feller, G. / Gerday, C. / Haser, R. #3: Journal: J.Mol.Biol. / Year: 1993 Title: Structure and Molecular Model Refinement of Pig Pancreatic Alpha-Amylase at 2.1 A Resolution Authors: Qian, M. / Haser, R. / Payan, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1aqm.cif.gz | 124.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1aqm.ent.gz | 101.7 KB | Display | PDB format |
PDBx/mmJSON format | 1aqm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aq/1aqm ftp://data.pdbj.org/pub/pdb/validation_reports/aq/1aqm | HTTPS FTP |
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-Related 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: A23 / Cell line: RR1 / Gene: AMY / Organ: PANCREAS / Cell line (production host): RR1 / Production host: Escherichia coli (E. coli) / References: UniProt: P29957, alpha-amylase |
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#2: Chemical | ChemComp-CA / |
#3: Chemical | ChemComp-CL / |
#4: Chemical | ChemComp-TRS / |
#5: 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: 2.91 Å3/Da / Density % sol: 58 % | |||||||||||||||
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Crystal grow | pH: 7 / Details: pH 7.0 | |||||||||||||||
Crystal grow | *PLUS Temperature: 4, 20 ℃ / Method: vapor diffusion, hanging drop / Details: prtein to mother liquor ration was 2:1 / PH range low: 7.1 / PH range high: 6.8 | |||||||||||||||
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 RUH2R / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 1, 1996 / Details: COLLIMATOR |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→43 Å / Num. obs: 42049 / % possible obs: 85.9 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rsym value: 0.085 / Net I/σ(I): 8.3 |
Reflection shell | Resolution: 1.85→1.95 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 1.5 / Rsym value: 0.499 / % possible all: 61.8 |
Reflection | *PLUS Num. measured all: 153351 / Rmerge(I) obs: 0.085 |
Reflection shell | *PLUS % possible obs: 61.8 % / Rmerge(I) obs: 0.499 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PORCINE PANCREAS ALPHA-AMYLASE (QIAN ET AL. J.MOL.BIOL. 231, 785-799 (1993)) Resolution: 1.85→43 Å / Rfactor Rfree error: 0.002 / 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, TOPOLOGY AND PARAMETER INPUTS FOR THE TRIS ARE FOUND IN THE FIVE RESIDUES IN THE C-TERMINAL END OF THE ENZYME ARE ...Details: BULK SOLVENT REFINEMENT HAS BEEN APPLIED THROUGHOUT THE REFINEMENT PROCESS, TOPOLOGY AND PARAMETER INPUTS FOR THE TRIS ARE FOUND IN THE FIVE RESIDUES IN THE C-TERMINAL END OF THE ENZYME ARE NOT INCLUDED IN THE MODEL AS NO ELECTRON DENSITY WAS PRESENT FOR THESE RESIDUES. DOUBLE CONFORMATIONS HAVE BEEN ASSIGNED TO FOUR RESIDUES: THR 85, LEU 142, LEU 219 AND ARG 373. THE MISSING ATOMS OF GLU 118 IS DUE TO WEAK ELECTRON DENSITY
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Refinement step | Cycle: LAST / Resolution: 1.85→43 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.86→1.94 Å / Rfactor Rfree error: 0.021 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.334 |