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Yorodumi- PDB-6vsp: Structure of Serratia marcescens 2,3-butanediol dehydrogenase mut... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6vsp | ||||||
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Title | Structure of Serratia marcescens 2,3-butanediol dehydrogenase mutant Q247A | ||||||
Components | 2,3-butanediol dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / BDH | ||||||
Function / homology | Function and homology information Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / oxidoreductase activity Similarity search - Function | ||||||
Biological species | Serratia marcescens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Alahuhta, P.M. / Lunin, V.V. | ||||||
Funding support | United States, 1items
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Citation | Journal: Biotechnol Biofuels / Year: 2020 Title: Phylogenetics-based identification and characterization of a superior 2,3-butanediol dehydrogenase for Zymomonas mobilis expression. Authors: Subramanian, V. / Lunin, V.V. / Farmer, S.J. / Alahuhta, M. / Moore, K.T. / Ho, A. / Chaudhari, Y.B. / Zhang, M. / Himmel, M.E. / Decker, S.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6vsp.cif.gz | 131.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6vsp.ent.gz | 95.6 KB | Display | PDB format |
PDBx/mmJSON format | 6vsp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6vsp_validation.pdf.gz | 492.9 KB | Display | wwPDB validaton report |
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Full document | 6vsp_full_validation.pdf.gz | 494.6 KB | Display | |
Data in XML | 6vsp_validation.xml.gz | 2.1 KB | Display | |
Data in CIF | 6vsp_validation.cif.gz | 10.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vs/6vsp ftp://data.pdbj.org/pub/pdb/validation_reports/vs/6vsp | HTTPS FTP |
-Related structure data
Related structure data | 6xewC 6xexC 6vsm S: Starting model for refinement C: citing same article (ref.) |
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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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 27882.711 Da / Num. of mol.: 2 / Mutation: Q247A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Serratia marcescens (bacteria) / Gene: budC, A8A12_06140, FG174_10665 / Production host: Zymomonas mobilis (bacteria) References: UniProt: H9XP47, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor |
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-Non-polymers , 6 types, 552 molecules
#2: Chemical | #3: Chemical | ChemComp-GOL / | #4: Chemical | ChemComp-EDO / #5: Chemical | #6: Chemical | ChemComp-ADP / | #7: 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: 2.34 Å3/Da / Density % sol: 47.33 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M sodium malonate, pH 6-7, 6-15% w/v PEG3350 / PH range: 6-7 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54178 Å |
Detector | Type: Bruker Platinum 135 / Detector: CCD / Date: Nov 16, 2017 / Details: HELIOS MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 39724 / % possible obs: 100 % / Redundancy: 17.32 % / Rsym value: 0.1087 / Net I/σ(I): 18.67 |
Reflection shell | Resolution: 1.9→2 Å / Mean I/σ(I) obs: 2.58 / Num. unique obs: 5531 / Rsym value: 0.7479 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 6VSM 6vsm Resolution: 1.9→50 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.932 / SU B: 3.912 / SU ML: 0.108 / Cross valid method: FREE R-VALUE / ESU R: 0.155 / ESU R Free: 0.148 Details: Hydrogens have been added in their 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.012 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→50 Å
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Refine LS restraints |
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LS refinement shell |
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