+Open data
-Basic information
Entry | Database: PDB / ID: 8tdf | ||||||
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Title | Structure of Alistipes sp. Glucoside-3-dehydrogenase AL3 | ||||||
Components | Dehydrogenase | ||||||
Keywords | ISOMERASE / Oxidoreductase / Dehydrogenase | ||||||
Function / homology | Gfo/Idh/MocA-like oxidoreductase, bacterial type, C-terminal / Oxidoreductase family, C-terminal alpha/beta domain / Gfo/Idh/MocA-like oxidoreductase, N-terminal / Oxidoreductase family, NAD-binding Rossmann fold / Twin-arginine translocation pathway, signal sequence, bacterial/archaeal / NAD(P)-binding domain superfamily / nucleotide binding / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Dehydrogenase Function and homology information | ||||||
Biological species | Alistipes (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Lazarski, A.C. / Worrall, L.J. / Strynadka, N.C.J. | ||||||
Funding support | Canada, 1items
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Citation | Journal: Nature / Year: 2024 Title: An alternative broad-specificity pathway for glycan breakdown in bacteria. Authors: Nasseri, S.A. / Lazarski, A.C. / Lemmer, I.L. / Zhang, C.Y. / Brencher, E. / Chen, H.M. / Sim, L. / Panwar, D. / Betschart, L. / Worrall, L.J. / Brumer, H. / Strynadka, N.C.J. / Withers, S.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8tdf.cif.gz | 725.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8tdf.ent.gz | 604.8 KB | Display | PDB format |
PDBx/mmJSON format | 8tdf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/td/8tdf ftp://data.pdbj.org/pub/pdb/validation_reports/td/8tdf | HTTPS FTP |
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-Related structure data
Related structure data | 8tcdC 8tcrC 8tcsC 8tctC 8tdaC 8tdeC 8tdhC 8tdiC 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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Unit cell |
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-Components
#1: Protein | Mass: 52510.754 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Alistipes (bacteria) / Gene: A3BBH6_04580 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A4Y1WH70 #2: Chemical | ChemComp-NAD / #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.55 Å3/Da / Density % sol: 51.67 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.15 M Sodium Malonate 19% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9537 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 11, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→48 Å / Num. obs: 123819 / % possible obs: 99.7 % / Redundancy: 6.6 % / CC1/2: 0.994 / Rmerge(I) obs: 0.174 / Rpim(I) all: 0.073 / Rrim(I) all: 0.189 / Χ2: 0.99 / Net I/σ(I): 7.2 / Num. measured all: 822967 |
Reflection shell | Resolution: 2.1→2.14 Å / % possible obs: 99.7 % / Redundancy: 6.9 % / Rmerge(I) obs: 1.619 / Num. measured all: 41507 / Num. unique obs: 6021 / CC1/2: 0.513 / Rpim(I) all: 0.659 / Rrim(I) all: 1.75 / Χ2: 1.05 / Net I/σ(I) obs: 1.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→48 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.944 / SU B: 13.269 / SU ML: 0.165 / Cross valid method: THROUGHOUT / ESU R: 0.215 / ESU R Free: 0.177 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 51.456 Å2
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Refinement step | Cycle: 1 / Resolution: 2.1→48 Å
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Refine LS restraints |
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