+Open data
-Basic information
Entry | Database: PDB / ID: 6xew | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of Serratia marcescens 2,3-butanediol dehydrogenase | ||||||
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: 2 Å | ||||||
Authors | Alahuhta, P.M. / Lunin, V.V. | ||||||
Funding support | United States, 1items
| ||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6xew.cif.gz | 126.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6xew.ent.gz | 92 KB | Display | PDB format |
PDBx/mmJSON format | 6xew.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xe/6xew ftp://data.pdbj.org/pub/pdb/validation_reports/xe/6xew | HTTPS FTP |
---|
-Related structure data
Related structure data | 6vspC 6xexC 4ni5S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 27939.762 Da / Num. of mol.: 2 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 |
---|
-Non-polymers , 5 types, 443 molecules
#2: Chemical | #3: Chemical | ChemComp-HBR / | #4: Chemical | ChemComp-HBS / | #5: Chemical | ChemComp-ADP / | #6: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 43.3 % |
---|---|
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 |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54178 Å |
Detector | Type: Bruker Platinum 135 / Detector: CCD / Date: Mar 23, 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: 2→50 Å / Num. obs: 33823 / % possible obs: 100 % / Redundancy: 11.42 % / Rsym value: 0.1377 / Net I/σ(I): 11.23 |
Reflection shell | Resolution: 2→2.1 Å / Redundancy: 8.77 % / Mean I/σ(I) obs: 1.96 / Num. unique obs: 4496 / Rsym value: 0.6889 / % possible all: 100 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4NI5 Resolution: 2→45.335 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.942 / SU B: 4.525 / SU ML: 0.12 / Cross valid method: FREE R-VALUE / ESU R: 0.179 / ESU R Free: 0.16 Details: Hydrogens have been added in their riding positions
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.025 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→45.335 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|