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Yorodumi- PDB-8cqg: Crystal Structure of a Chimeric Alpha-Amylase from Pseudoalteromo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8cqg | |||||||||||||||
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Title | Crystal Structure of a Chimeric Alpha-Amylase from Pseudoalteromonas Haloplanktis | |||||||||||||||
Components | Alpha-amylase | |||||||||||||||
Keywords | HYDROLASE / APO / Alpha-Amylase / Chimeric | |||||||||||||||
Function / homology | Function and homology information alpha-amylase / alpha-amylase activity / carbohydrate metabolic process / extracellular space / metal ion binding Similarity search - Function | |||||||||||||||
Biological species | Pseudoalteromonas haloplanktis (bacteria) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å | |||||||||||||||
Authors | Skagseth, S. / Lund, B.A. / Griese, J.J. / van der Ent, F. / Aqvist, J. | |||||||||||||||
Funding support | Sweden, Norway, 4items
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Citation | Journal: Sci Adv / Year: 2023 Title: Computational design of the temperature optimum of an enzyme reaction. Authors: van der Ent, F. / Skagseth, S. / Lund, B.A. / Socan, J. / Griese, J.J. / Brandsdal, B.O. / Aqvist, J. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8cqg.cif.gz | 182.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8cqg.ent.gz | 146.9 KB | Display | PDB format |
PDBx/mmJSON format | 8cqg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8cqg_validation.pdf.gz | 437.3 KB | Display | wwPDB validaton report |
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Full document | 8cqg_full_validation.pdf.gz | 438 KB | Display | |
Data in XML | 8cqg_validation.xml.gz | 21.4 KB | Display | |
Data in CIF | 8cqg_validation.cif.gz | 33.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cq/8cqg ftp://data.pdbj.org/pub/pdb/validation_reports/cq/8cqg | HTTPS FTP |
-Related structure data
Related structure data | 8cqfC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 49230.035 Da / Num. of mol.: 1 Mutation: A77V Q204L S226G T227A E228K N231T T232L G270_G271insA A272G G273S N274S V275I I276L D310N T311D D312W Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudoalteromonas haloplanktis (bacteria) Gene: amy / Production host: Escherichia coli (E. coli) / Strain (production host): NiCo21(DE3) / References: UniProt: P29957, alpha-amylase | ||||||||
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#2: Chemical | ChemComp-EDO / #3: Chemical | #4: Chemical | ChemComp-CA / | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.65 Å3/Da / Density % sol: 66.3 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 3 M NaCl, 0.1 M BisTris |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97625 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 27, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 1.74→68.48 Å / Num. obs: 74537 / % possible obs: 99.7 % / Redundancy: 6.7 % / CC1/2: 0.998 / Net I/σ(I): 12.8 |
Reflection shell | Resolution: 1.74→1.77 Å / Num. unique obs: 3893 / CC1/2: 0.363 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.74→68.48 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.94 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.74→68.48 Å
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Refine LS restraints |
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LS refinement shell |
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