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Yorodumi- PDB-4e5m: Thermostable phosphite dehydrogenase E175A/A176R in complex with NADP -
+Open data
-Basic information
Entry | Database: PDB / ID: 4e5m | ||||||
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Title | Thermostable phosphite dehydrogenase E175A/A176R in complex with NADP | ||||||
Components | Thermostable phosphite dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / D-2-hydroxyacid dehydrogenase | ||||||
Function / homology | Function and homology information phosphonate dehydrogenase / phosphonate dehydrogenase activity / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / NAD binding Similarity search - Function | ||||||
Biological species | Pseudomonas stutzeri (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Zou, Y. / Zhang, H. / Nair, S.K. | ||||||
Citation | Journal: Biochemistry / Year: 2012 Title: Crystal structures of phosphite dehydrogenase provide insights into nicotinamide cofactor regeneration. Authors: Zou, Y. / Zhang, H. / Brunzelle, J.S. / Johannes, T.W. / Woodyer, R. / Hung, J.E. / Nair, N. / van der Donk, W.A. / Zhao, H. / Nair, S.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4e5m.cif.gz | 146.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4e5m.ent.gz | 115 KB | Display | PDB format |
PDBx/mmJSON format | 4e5m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e5/4e5m ftp://data.pdbj.org/pub/pdb/validation_reports/e5/4e5m | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 35938.367 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas stutzeri (bacteria) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O69054*PLUS #2: Chemical | #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: 2.24 Å3/Da / Density % sol: 45.08 % |
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Crystal grow | Temperature: 285 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 25-30% PEG 3350, 100 mM KCl, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 285K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D |
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Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.85→50 Å / Num. obs: 51959 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Redundancy: 4.3 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 19.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 12X phosphite dehydrogenase E175A Resolution: 1.85→25 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.928 / SU B: 2.771 / SU ML: 0.086 / Cross valid method: THROUGHOUT / ESU R: 0.163 / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.838 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.899 Å / Total num. of bins used: 20
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