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Yorodumi- PDB-8xxa: Rhodothermus marinus alpha-amylase RmGH13_47A CBM48-A-B-C domains... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8xxa | ||||||
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Title | Rhodothermus marinus alpha-amylase RmGH13_47A CBM48-A-B-C domains in complex with branched pentasaccharide | ||||||
Components | alpha-amylase | ||||||
Keywords | HYDROLASE / alpha-amylase / (beta/alpha)8 barrel / CARBOHYDRATE | ||||||
Function / homology | alpha-maltotriose / : / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL Function and homology information | ||||||
Biological species | Rhodothermus marinus JCM 9785 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å | ||||||
Authors | Tonozuka, T. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Proteins / Year: 2024 Title: Structural basis for the recognition of alpha-1,6-branched alpha-glucan by GH13_47 alpha-amylase from Rhodothermus marinus. Authors: Miyasaka, Y. / Yokoyama, K. / Kozono, T. / Kitano, Y. / Miyazaki, T. / Sakaguchi, M. / Nishikawa, A. / Tonozuka, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8xxa.cif.gz | 165.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8xxa.ent.gz | 122.5 KB | Display | PDB format |
PDBx/mmJSON format | 8xxa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8xxa_validation.pdf.gz | 2.1 MB | Display | wwPDB validaton report |
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Full document | 8xxa_full_validation.pdf.gz | 2.1 MB | Display | |
Data in XML | 8xxa_validation.xml.gz | 30.5 KB | Display | |
Data in CIF | 8xxa_validation.cif.gz | 48.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xx/8xxa ftp://data.pdbj.org/pub/pdb/validation_reports/xx/8xxa | HTTPS FTP |
-Related structure data
Related structure data | 8xx9C 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 75351.531 Da / Num. of mol.: 1 / Mutation: D563A Source method: isolated from a genetically manipulated source Details: DDBJ accession code LC794559 Source: (gene. exp.) Rhodothermus marinus JCM 9785 (bacteria) Production host: Escherichia coli (E. coli) / References: alpha-amylase |
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-Sugars , 2 types, 2 molecules
#2: Polysaccharide | alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-6)-[alpha-D-glucopyranose-(1-4)]alpha-D- ...alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-6)-[alpha-D-glucopyranose-(1-4)]alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose Type: oligosaccharide / Mass: 828.719 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source |
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#3: Polysaccharide | alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose |
-Non-polymers , 7 types, 720 molecules
#4: Chemical | ChemComp-MN / | ||
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#5: Chemical | ChemComp-CA / | ||
#6: Chemical | ChemComp-MES / | ||
#7: Chemical | ChemComp-PGE / | ||
#8: Chemical | ChemComp-PEG / | ||
#9: Chemical | #10: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 50.91 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: MES buffer, PEG 20000, PEG 4000, PEG 3350, sodium iodide |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Dec 6, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→47.9 Å / Num. obs: 106919 / % possible obs: 98.8 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.032 / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 1.55→1.58 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 5315 / Rpim(I) all: 0.258 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→47.94 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.964 / Cross valid method: THROUGHOUT / ESU R: 0.076 / ESU R Free: 0.072 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.582 Å2
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Refinement step | Cycle: 1 / Resolution: 1.55→47.94 Å
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