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Yorodumi- PDB-8i29: Crystal structure of butanol dehydrogenase A (YqdH) in complex wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8i29 | |||||||||
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Title | Crystal structure of butanol dehydrogenase A (YqdH) in complex with NADH from Fusobacterium nucleatum | |||||||||
Components | NADH-dependent butanol dehydrogenase A | |||||||||
Keywords | BIOSYNTHETIC PROTEIN / YqdH / NADH | |||||||||
Function / homology | Function and homology information alcohol dehydrogenase [NAD(P)+] activity / butanol dehydrogenase (NAD+) activity / methylglyoxal reductase (NADPH) (acetol producing) activity / alcohol dehydrogenase (NADP+) activity / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / nucleotide binding / metal ion binding / cytosol Similarity search - Function | |||||||||
Biological species | Fusobacterium nucleatum subsp. nucleatum ATCC 25586 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.72 Å | |||||||||
Authors | Bai, X. / Lan, J. / Bu, T.T. / Wang, L.L. / He, S.R. / Zhang, J. / Xu, Y.B. | |||||||||
Funding support | Korea, Republic Of, 1items
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Citation | Journal: To Be Published Title: Crystal structure of butanol dehydrogenase A (YqdH) in complex with NADH from Fusobacterium nucleatum Authors: Bai, X. / Lan, J. / Bu, T.T. / He, S.R. / Zhang, J. / Wang, L.L. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8i29.cif.gz | 92.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8i29.ent.gz | 67.9 KB | Display | PDB format |
PDBx/mmJSON format | 8i29.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8i29_validation.pdf.gz | 681.6 KB | Display | wwPDB validaton report |
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Full document | 8i29_full_validation.pdf.gz | 687.9 KB | Display | |
Data in XML | 8i29_validation.xml.gz | 17.2 KB | Display | |
Data in CIF | 8i29_validation.cif.gz | 23.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i2/8i29 ftp://data.pdbj.org/pub/pdb/validation_reports/i2/8i29 | HTTPS FTP |
-Related structure data
Related structure data | 6l1kS S: Starting model for refinement |
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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: 43336.102 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Fusobacterium nucleatum subsp. nucleatum ATCC 25586 (bacteria) Gene: FN1415 / Production host: Escherichia coli K-12 (bacteria) References: UniProt: Q8R612, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor |
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-Non-polymers , 5 types, 70 molecules
#2: Chemical | ChemComp-CO / |
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#3: Chemical | ChemComp-NAD / |
#4: Chemical | ChemComp-CL / |
#5: Chemical | ChemComp-PO4 / |
#6: Water | ChemComp-HOH / |
-Details
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: 3.14 Å3/Da / Density % sol: 60.83 % |
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Crystal grow | Temperature: 279.15 K / Method: vapor diffusion, hanging drop / Details: ammonium phosphate, HEPES |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17B1 / Wavelength: 0.9796 Å |
Detector | Type: DECTRIS PILATUS3 X CdTe 2M / Detector: PIXEL / Date: May 26, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9796 Å / Relative weight: 1 |
Reflection | Resolution: 2.719→35.53 Å / Num. obs: 14920 / % possible obs: 98.64 % / Redundancy: 12.4 % / CC1/2: 0.929 / CC star: 0.981 / Net I/σ(I): 11.88 |
Reflection shell | Resolution: 2.719→2.817 Å / Num. unique obs: 752 / CC1/2: 0.531 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6L1K Resolution: 2.72→35.53 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.906 / SU B: 14.462 / SU ML: 0.286 / Cross valid method: THROUGHOUT / ESU R: 1.016 / ESU R Free: 0.352 / 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: 56.195 Å2
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Refinement step | Cycle: 1 / Resolution: 2.72→35.53 Å
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Refine LS restraints |
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