+Open data
-Basic information
Entry | Database: PDB / ID: 1aqh | ||||||
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Title | ALPHA-AMYLASE FROM ALTEROMONAS HALOPLANCTIS | ||||||
Components | ALPHA-AMYLASE | ||||||
Keywords | HYDROLASE / ALPHA-AMYLASE / ALPHA-1 / 4-GLUCAN-4-GLUCANOHYDROLASE / BETA-ALPHA-EIGHT BARREL / PSYCHROPHILIC ENZYME | ||||||
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 / PHASES FROM ALPHA-AMYLASE COMPLEXED WITH A TRIS MOLECULE COMBINED WITH STRUCTURE FACTORS FROM THIS NATIVE DATA SET / Resolution: 2 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: Protein Sci. / Year: 1998 Title: Erratum. 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. #2: 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1aqh.cif.gz | 122.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1aqh.ent.gz | 100 KB | Display | PDB format |
PDBx/mmJSON format | 1aqh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aq/1aqh ftp://data.pdbj.org/pub/pdb/validation_reports/aq/1aqh | 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 / 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: 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 % Description: THE TRIS MOLECULE AND WATER MOLECULES IN AND AROUND THE ACTIVE SITE WAS NOT INCLUDED IN THE PHASE INFORMATION | |||||||||||||||
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Crystal grow | pH: 7 / Details: pH 7.0 | |||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop / 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: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 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: 2→43 Å / Num. obs: 31485 / % possible obs: 80.5 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Rsym value: 0.142 / Net I/σ(I): 5 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 1.3 % / Mean I/σ(I) obs: 1.1 / Rsym value: 0.569 / % possible all: 31.5 |
Reflection | *PLUS Num. measured all: 93724 / Rmerge(I) obs: 0.142 |
Reflection shell | *PLUS % possible obs: 31.5 % / Rmerge(I) obs: 0.142 |
-Processing
Software |
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Refinement | Method to determine structure: PHASES FROM ALPHA-AMYLASE COMPLEXED WITH A TRIS MOLECULE COMBINED WITH STRUCTURE FACTORS FROM THIS NATIVE DATA SET Resolution: 2→43 Å / Rfactor Rfree error: 0.0037 / 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
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Refinement step | Cycle: LAST / Resolution: 2→43 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.09 Å / Rfactor Rfree error: 0.03 / 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: 0.319 |