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- PDB-6jx1: Crystal structure of Formate dehydrogenase mutant V198I/C256I/P26... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6jx1 | ||||||
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Title | Crystal structure of Formate dehydrogenase mutant V198I/C256I/P260S/E261P/S381N/S383F from Pseudomonas sp. 101 | ||||||
![]() | Formate dehydrogenase | ||||||
![]() | OXIDOREDUCTASE / Formate Dehydrogenase | ||||||
Function / homology | ![]() formate catabolic process / formate dehydrogenase / formate dehydrogenase (NAD+) activity / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / NAD binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Feng, Y. / Xue, S. / Guo, X. / Zhao, Z. | ||||||
![]() | ![]() Title: Structure-Guided Design of Formate Dehydrogenase for Regeneration of a Non-Natural Redox Cofactor. Authors: Guo, X. / Wang, X. / Liu, Y. / Li, Q. / Wang, J. / Liu, W. / Zhao, Z.K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 159.7 KB | Display | ![]() |
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PDB format | ![]() | 124.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 450.6 KB | Display | ![]() |
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Full document | ![]() | 456.7 KB | Display | |
Data in XML | ![]() | 28.9 KB | Display | |
Data in CIF | ![]() | 40.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6jujC ![]() 6jukC ![]() 6jwgC ![]() 2go1S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 44263.215 Da / Num. of mol.: 2 / Mutation: V198I/C256I/H260S/E261P/S381N/S383F Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-GOL / | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.87 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.2 M Sodium acetate trihydrate, 0.1 M Sodium cacodylate trihydrate pH 6.5, 30% w/v Polyethylene glycol 8,000. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 130 mm / Detector: CCD / Date: Dec 28, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.23→50 Å / Num. obs: 27557 / % possible obs: 74.62 % / Redundancy: 2.7 % / Biso Wilson estimate: 28.54 Å2 / CC1/2: 0.879 / Rmerge(I) obs: 0.23 / Net I/av σ(I): 4.33 / Net I/σ(I): 4.33 |
Reflection shell | Resolution: 2.23→2.31 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 1.68 / Num. unique obs: 1285 / CC1/2: 0.908 / % possible all: 35.56 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2GO1 Resolution: 2.233→42.772 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.82
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.233→42.772 Å
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Refine LS restraints |
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LS refinement shell |
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