+Open data
-Basic information
Entry | Database: PDB / ID: 4ebf | ||||||
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Title | SeMet thermostable phosphite dehydrogenase Glu175-Ala mutant | ||||||
Components | Thermostable phosphite dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / D-2-hydroxyacid dehydrogenase | ||||||
Function / homology | Function and homology information phosphonate dehydrogenase / phosphonate dehydrogenase activity / hydroxypyruvate reductase (NADH) activity / hydroxypyruvate reductase [NAD(P)H] activity / glyoxylate reductase (NADPH) activity / NAD binding / cytosol Similarity search - Function | ||||||
Biological species | Pseudomonas stutzeri (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 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 | 4ebf.cif.gz | 388.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ebf.ent.gz | 331.3 KB | Display | PDB format |
PDBx/mmJSON format | 4ebf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ebf_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 4ebf_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 4ebf_validation.xml.gz | 80 KB | Display | |
Data in CIF | 4ebf_validation.cif.gz | 110 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eb/4ebf ftp://data.pdbj.org/pub/pdb/validation_reports/eb/4ebf | HTTPS FTP |
-Related 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: 36649.039 Da / Num. of mol.: 6 / Mutation: Thermostable variant, E175A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas stutzeri (bacteria) / Gene: ptx / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O69054*PLUS #2: Chemical | ChemComp-NAD / #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: 2.63 Å3/Da / Density % sol: 53.16 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 25-30% PEG 3350, 100 mM KCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. all: 98877 / Num. obs: 98877 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Redundancy: 4.1 % / Rsym value: 0.082 / Net I/σ(I): 19.4 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 3.9 / Rsym value: 0.373 / % possible all: 98.3 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.3→25 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.898 / SU B: 8.644 / SU ML: 0.21 / Cross valid method: THROUGHOUT / ESU R: 0.371 / ESU R Free: 0.27 / 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: 40.159 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.362 Å / Total num. of bins used: 20
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