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Yorodumi- PDB-6ih8: Crystal structure of Phosphite Dehydrogenase mutant I151R/P176R/M... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ih8 | ||||||
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Title | Crystal structure of Phosphite Dehydrogenase mutant I151R/P176R/M207A from Ralstonia sp. 4506 | ||||||
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: 2.25 Å | ||||||
Authors | Song, X. / Feng, Y. / Liu, Y. / Zhao, Z. | ||||||
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 | 6ih8.cif.gz | 269.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ih8.ent.gz | 217.6 KB | Display | PDB format |
PDBx/mmJSON format | 6ih8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ih8_validation.pdf.gz | 458.2 KB | Display | wwPDB validaton report |
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Full document | 6ih8_full_validation.pdf.gz | 471.2 KB | Display | |
Data in XML | 6ih8_validation.xml.gz | 51.9 KB | Display | |
Data in CIF | 6ih8_validation.cif.gz | 74.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ih/6ih8 ftp://data.pdbj.org/pub/pdb/validation_reports/ih/6ih8 | HTTPS FTP |
-Related structure data
Related structure data | 6ih2C 6ih3C 6ih4C 6ih5C 6ih6C 4e5mS 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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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 36913.699 Da / Num. of mol.: 4 / Mutation: I151R, P176R,M207A 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: 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: 2.45 Å3/Da / Density % sol: 49.73 % |
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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: BL17U / Wavelength: 0.9798 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Dec 15, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9798 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→26.75 Å / Num. obs: 67160 / % possible obs: 98.99 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 4.8 |
Reflection shell | Resolution: 2.25→2.33 Å / Rmerge(I) obs: 0.53 / Num. unique obs: 6292 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4E5M Resolution: 2.25→26.749 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.11
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.25→26.749 Å
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Refine LS restraints |
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LS refinement shell |
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