+Open data
-Basic information
Entry | Database: PDB / ID: 4nu6 | ||||||
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Title | Crystal Structure of PTDH R301K | ||||||
Components | Phosphonate dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / Protein / Rossmann Fold / Phosphite Dehydrogenase / Dehydrogenation / Cystoplasm | ||||||
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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.65 Å | ||||||
Authors | Nair, S.K. / Chekan, J.R. | ||||||
Citation | Journal: Plos One / Year: 2014 Title: Chemical rescue and inhibition studies to determine the role of arg301 in phosphite dehydrogenase. Authors: Hung, J.E. / Fogle, E.J. / Garg, N. / Chekan, J.R. / Nair, S.K. / van der Donk, W.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4nu6.cif.gz | 138.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4nu6.ent.gz | 110.4 KB | Display | PDB format |
PDBx/mmJSON format | 4nu6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nu/4nu6 ftp://data.pdbj.org/pub/pdb/validation_reports/nu/4nu6 | 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: 35883.324 Da / Num. of mol.: 2 / Mutation: R301K Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas stutzeri (bacteria) / Gene: ptxD / Production host: Escherichia coli (E. coli) / References: UniProt: O69054, phosphonate dehydrogenase #2: Chemical | #3: Chemical | #4: 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: 2.71 Å3/Da / Density % sol: 54.57 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 5.8 Details: 0.1 M NaCl, 16% PEG 6,000, 0.1 M Sodium Cacodylate, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 288K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 24, 2013 |
Radiation | Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→50 Å / Num. all: 23441 / Num. obs: 23441 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Rsym value: 0.107 / Net I/σ(I): 13.7 |
Reflection shell | Resolution: 2.65→2.7 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 2.15 / Num. unique all: 1127 / Rsym value: 0.668 / % possible all: 100 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.65→25 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.901 / Occupancy max: 1 / Occupancy min: 1 / SU B: 11.936 / SU ML: 0.244 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.724 / ESU R Free: 0.344 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 127.48 Å2 / Biso mean: 39.29 Å2 / Biso min: 14.53 Å2
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Refinement step | Cycle: LAST / Resolution: 2.65→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.65→2.718 Å / Total num. of bins used: 20
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