+Open data
-Basic information
Entry | Database: PDB / ID: 8dl1 | |||||||||
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Title | BoGH13ASus-E523Q from Bacteroides ovatus bound to maltoheptaose | |||||||||
Components | Alpha amylase, catalytic domain proteinAlpha-amylase | |||||||||
Keywords | HYDROLASE / alpha-amylase / starch / GH13 / glycoside hydrolase | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Bacteroides ovatus ATCC 8483 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å | |||||||||
Authors | Brown, H.A. / DeVeaux, A.L. / Koropatkin, N.M. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Cell.Mol.Life Sci. / Year: 2023 Title: BoGH13A Sus from Bacteroides ovatus represents a novel alpha-amylase used for Bacteroides starch breakdown in the human gut. Authors: Brown, H.A. / DeVeaux, A.L. / Juliano, B.R. / Photenhauer, A.L. / Boulinguiez, M. / Bornschein, R.E. / Wawrzak, Z. / Ruotolo, B.T. / Terrapon, N. / Koropatkin, N.M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8dl1.cif.gz | 632.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8dl1.ent.gz | 514.5 KB | Display | PDB format |
PDBx/mmJSON format | 8dl1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dl/8dl1 ftp://data.pdbj.org/pub/pdb/validation_reports/dl/8dl1 | HTTPS FTP |
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-Related structure data
Related structure data | 8dgeSC 8dl2C S: Starting model for refinement 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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2 |
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3 |
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4 |
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Unit cell |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 84054.641 Da / Num. of mol.: 4 / Mutation: E523Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides ovatus ATCC 8483 (bacteria) Strain: ATCC 8483 / DSM 1896 / JCM 5824 / BCRC 10623 / CCUG 4943 / NCTC 11153 Gene: BACOVA_03514,Bovatus_03803 / Production host: Escherichia coli (E. coli) / References: UniProt: A7M087 |
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-Sugars , 7 types, 12 molecules
#2: Polysaccharide | alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D- ...alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose Source method: isolated from a genetically manipulated source #3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Polysaccharide | alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose | Source method: isolated from a genetically manipulated source #5: 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)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose | Type: oligosaccharide / Mass: 1153.001 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source #6: 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)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose | Type: oligosaccharide / Mass: 1153.001 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source #7: 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)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose | Type: oligosaccharide / Mass: 990.860 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source #8: Polysaccharide | alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D- ...alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose | Source method: isolated from a genetically manipulated source |
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-Non-polymers , 10 types, 1960 molecules
#9: Chemical | ChemComp-EDO / #10: Chemical | ChemComp-ACT / #11: Chemical | ChemComp-CA / #12: Chemical | ChemComp-MN / #13: Chemical | ChemComp-1PE / | #14: Chemical | ChemComp-PGE / | #15: Chemical | ChemComp-NA / | #16: Chemical | ChemComp-PEG / | #17: Chemical | ChemComp-CL / | #18: Water | ChemComp-HOH / | |
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-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: 2.75 Å3/Da / Density % sol: 55.33 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 12% MPD, 12% PEG1000, 12% PEG3350, 0.1M Tris/Bicine pH 8.5, 0.08M ethylene glycols mix |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.033 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 6, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 |
Reflection | Resolution: 2.09→47.93 Å / Num. obs: 212239 / % possible obs: 98.7 % / Redundancy: 3.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.074 / Net I/σ(I): 10 |
Reflection shell | Resolution: 2.09→2.17 Å / Rmerge(I) obs: 1.12 / Num. unique obs: 21205 / CC1/2: 0.467 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 8DGE Resolution: 2.09→47.93 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.926 / SU B: 5.481 / SU ML: 0.136 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.191 / ESU R Free: 0.169 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 92.8 Å2 / Biso mean: 26.133 Å2 / Biso min: 6.76 Å2
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Refinement step | Cycle: final / Resolution: 2.09→47.93 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.09→2.144 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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