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Yorodumi- PDB-1e43: Native structure of chimaeric amylase from B. amyloliquefaciens a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1.0E+43 | ||||||
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Title | Native structure of chimaeric amylase from B. amyloliquefaciens and B. licheniformis at 1.7A | ||||||
Components | ALPHA-AMYLASE | ||||||
Keywords | HYDROLASE / AMYLASE / FAMILY 13 | ||||||
Function / homology | Function and homology information alpha-amylase / alpha-amylase activity / carbohydrate metabolic process / calcium ion binding / extracellular space / extracellular region Similarity search - Function | ||||||
Biological species | BACILLUS AMYLOLIQUEFACIENS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Brzozowski, A.M. / Lawson, D.M. / Turkenburg, J.P. / Bisgaard-Frantzen, H. / Svendsen, A. / Borchert, T.V. / Dauter, Z. / Wilson, K.S. / Davies, G.J. | ||||||
Citation | Journal: Biochemistry / Year: 2000 Title: Structural Analysis of a Chimeric Bacterial Alpha-Amylase. High Resolution Analysis of Native and Ligand Complexes Authors: Brzozowski, A.M. / Lawson, D.M. / Turkenburg, J.P. / Bisgaard-Frantzen, H. / Svendsen, A. / Borchert, T.V. / Dauter, Z. / Wilson, K.S. / Davies, G.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1e43.cif.gz | 134.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1e43.ent.gz | 101.7 KB | Display | PDB format |
PDBx/mmJSON format | 1e43.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e4/1e43 ftp://data.pdbj.org/pub/pdb/validation_reports/e4/1e43 | HTTPS FTP |
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-Related structure data
Related structure data | 1e3xSC 1e3zC 1e40C C: citing same article (ref.) 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: 55038.410 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: CHIMAERIC STRUCTURE CONSISTING OF RESIDUES 1 - 300 OF B. AMYLOLIQUEFACIENS AND RESIDUES 301 - 483 OF B. LICHENIFORMIS Source: (gene. exp.) BACILLUS AMYLOLIQUEFACIENS (bacteria) / Description: SYNTHETIC GENE / Production host: BACILLUS AMYLOLIQUEFACIENS (bacteria) / References: UniProt: P00692, UniProt: P06278, alpha-amylase | ||||
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#2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-NA / | #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: 2.34 Å3/Da / Density % sol: 47 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 10 Details: CRYSTALS WERE GROWN AT 18C USING THE HANGING DROP METHOD WITH 8-13% MONOMETHYL ETHER POLYETHYLENE GLYCOL 2000 OR 5000 AS PRECIPITANT. DROPS WERE BUFFERED WITH 0.1M TRIS/HCL PH 7.5 CONTAINING ...Details: CRYSTALS WERE GROWN AT 18C USING THE HANGING DROP METHOD WITH 8-13% MONOMETHYL ETHER POLYETHYLENE GLYCOL 2000 OR 5000 AS PRECIPITANT. DROPS WERE BUFFERED WITH 0.1M TRIS/HCL PH 7.5 CONTAINING 5MM CACL2 AND THE PROTEIN CONCENTRATION WAS 30-35MG/ML. | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9386 |
Detector | Type: ADSC-Q4 / Detector: CCD / Date: Sep 15, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9386 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→30 Å / Num. obs: 51292 / % possible obs: 98 % / Redundancy: 3 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 15 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.081 / Mean I/σ(I) obs: 13 / % possible all: 99 |
Reflection | *PLUS % possible obs: 98 % / Rmerge(I) obs: 0.07 |
Reflection shell | *PLUS Highest resolution: 1.7 Å / % possible obs: 99 % / Mean I/σ(I) obs: 13 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1E3X Resolution: 1.7→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.09 / ESU R Free: 0.1
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Displacement parameters | Biso mean: 10.2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→20 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.133 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: p_bond_d / Dev ideal: 0.01 |