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Yorodumi- PDB-6ih3: Crystal structure of Phosphite Dehydrogenase from Ralstonia sp. 4... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ih3 | ||||||
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Title | Crystal structure of Phosphite Dehydrogenase from Ralstonia sp. 4506 in complex with non-natural cofactor Nicotinamide Cytosine Dinucleotide | ||||||
Components | Phosphite dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / Phosphite Dehydrogenase | ||||||
Function / homology | Function and homology information hydroxypyruvate reductase (NADH) activity / hydroxypyruvate reductase [NAD(P)H] activity / glyoxylate reductase (NADPH) activity / NAD binding / cytosol Similarity search - Function | ||||||
Biological species | Ralstonia sp. 4506 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.942 Å | ||||||
Authors | Song, X. / Feng, Y. / Zhao, Z. / Liu, Y. | ||||||
Citation | Journal: Acs Catalysis / Year: 2019 Title: Structural Insights into Phosphite Dehydrogenase Variants Favoring a Non-natural Redox Cofactor Authors: Liu, Y. / Feng, Y. / Wang, L. / Guo, X. / Liu, W. / Li, Q. / Wang, X. / Xue, S. / Zhao, Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ih3.cif.gz | 157.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ih3.ent.gz | 121.4 KB | Display | PDB format |
PDBx/mmJSON format | 6ih3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ih/6ih3 ftp://data.pdbj.org/pub/pdb/validation_reports/ih/6ih3 | HTTPS FTP |
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-Related structure data
Related structure data | 6ih2C 6ih4C 6ih5C 6ih6C 6ih8C 4e5mS C: citing same article (ref.) 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: 36627.430 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ralstonia sp. 4506 (bacteria) / Gene: ptxD / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: G4XDR8 #2: Chemical | ChemComp-A7R / [[( | #3: Water | ChemComp-HOH / | |
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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: 2.52 Å3/Da / Density % sol: 51.23 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.2 M NaCl, 0.1 M Tris-HCl pH 8.0, 25% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9793 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Dec 24, 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: 1.94→45.41 Å / Num. obs: 55297 / % possible obs: 99.66 % / Redundancy: 12.7 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 15.05 |
Reflection shell | Resolution: 1.94→2.01 Å / Rmerge(I) obs: 0.56 / Num. unique obs: 5308 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4E5M Resolution: 1.942→45.408 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.84
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.942→45.408 Å
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Refine LS restraints |
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LS refinement shell |
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