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Yorodumi- PDB-8y46: Crystal structure of L-2-keto-3-deoxyfuconate 4-dehydrogenase bou... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8y46 | ||||||
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Title | Crystal structure of L-2-keto-3-deoxyfuconate 4-dehydrogenase bound to L-KDF or L-2,4-DKDF | ||||||
Components | SDR family oxidoreductase | ||||||
Keywords | OXIDOREDUCTASE / dehydrogenase / Rossmann Fold | ||||||
Function / homology | : / : / DI(HYDROXYETHYL)ETHER / : Function and homology information | ||||||
Biological species | Herbaspirillum huttiense (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.29 Å | ||||||
Authors | Akagashi, M. / Watanabe, S. | ||||||
Funding support | 1items
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Citation | Journal: Sci Rep / Year: 2024 Title: Crystal structure of L-2-keto-3-deoxyfuconate 4-dehydrogenase reveals a unique binding mode as a alpha-furanosyl hemiketal of substrates. Authors: Akagashi, M. / Watanabe, S. / Kwiatkowski, S. / Drozak, J. / Terawaki, S. / Watanabe, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8y46.cif.gz | 212.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8y46.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8y46.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8y46_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 8y46_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 8y46_validation.xml.gz | 45.6 KB | Display | |
Data in CIF | 8y46_validation.cif.gz | 67.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y4/8y46 ftp://data.pdbj.org/pub/pdb/validation_reports/y4/8y46 | HTTPS FTP |
-Related structure data
Related structure data | 8xwkC 8y11C 8y4bC 8y4jC 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: 27596.275 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Herbaspirillum huttiense (bacteria) / Gene: E2K99_19890 / Production host: Escherichia coli DH5[alpha] (bacteria) / References: UniProt: A0A4P7ABK7 |
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-Non-polymers , 5 types, 896 molecules
#2: Chemical | #3: Chemical | Mass: 162.141 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C6H10O5 / Feature type: SUBJECT OF INVESTIGATION #4: Chemical | ChemComp-A1LXB / | Mass: 160.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C6H8O5 / Feature type: SUBJECT OF INVESTIGATION #5: Chemical | #6: 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: 2.2 Å3/Da / Density % sol: 44.06 % |
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Crystal grow | Temperature: 293 K / Method: evaporation Details: 0.2 M Sodium acetate, 0.1 M Tris-HCl pH8.5, 25% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 293 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 29, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.29→44.99 Å / Num. obs: 230393 / % possible obs: 100 % / Redundancy: 17.82 % / CC1/2: 0.998 / Net I/σ(I): 17.1 |
Reflection shell | Resolution: 1.29→1.31 Å / Num. unique obs: 198053 / CC1/2: 0.88 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: AlphaFold Resolution: 1.29→44.99 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.36 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.29→44.99 Å
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Refine LS restraints |
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LS refinement shell |
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