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Yorodumi- PDB-6l1k: Crystal structure of NADH-dependent butanol dehydrogenase A from ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6l1k | |||||||||
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Title | Crystal structure of NADH-dependent butanol dehydrogenase A from Fusobacterium nucleatum | |||||||||
Components | NADH-dependent butanol dehydrogenase A | |||||||||
Keywords | OXIDOREDUCTASE / Butanol dehydrogenase / FnYqdH / Fusobacterium nucleatum | |||||||||
Function / homology | Function and homology information alcohol dehydrogenase [NAD(P)+] activity / methylglyoxal reductase (NADPH) (acetol producing) activity / butanol dehydrogenase (NAD+) 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 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å | |||||||||
Authors | Lan, J. / Shang, F. / Liu, W. / Xu, Y. / Chen, Y. | |||||||||
Funding support | China, 2items
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Citation | Journal: To Be Published Title: Crystal structure of NADH-dependent butanol dehydrogenase A from Fusobacterium nucleatum Authors: Lan, J. / Shang, F. / Liu, W. / Xu, Y. / Chen, Y. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6l1k.cif.gz | 116.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6l1k.ent.gz | 71.5 KB | Display | PDB format |
PDBx/mmJSON format | 6l1k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l1/6l1k ftp://data.pdbj.org/pub/pdb/validation_reports/l1/6l1k | HTTPS FTP |
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-Related structure data
Related structure data | 1vljS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#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 (strain ATCC 25586 / CIP 101130 / JCM 8532 / LMG 13131) (bacteria) Strain: ATCC 25586 / CIP 101130 / JCM 8532 / LMG 13131 / Gene: FN1415 / Production host: Escherichia coli (E. coli) References: UniProt: Q8R612, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor |
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#2: Chemical | ChemComp-PO4 / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.18 Å3/Da / Density % sol: 61.32 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop Details: 2.0M Ammonium phosphate monobasic, 0.1M TRIS hydrochloride pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9793 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 24, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 1.97→50 Å / Num. obs: 39074 / % possible obs: 100 % / Redundancy: 6.6 % / Biso Wilson estimate: 24.49 Å2 / Rsym value: 0.061 / Net I/σ(I): 21.37 |
Reflection shell | Resolution: 1.98→2.01 Å / Num. unique obs: 39063 / Rsym value: 0.469 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1VLJ Resolution: 1.97→39.42 Å / SU ML: 0.1748 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.8434
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.01 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.97→39.42 Å
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Refine LS restraints |
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LS refinement shell |
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