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Yorodumi- PDB-5n2i: F420:NADPH oxidoreductase from Thermobifida fusca with NADP+ bound -
+Open data
-Basic information
Entry | Database: PDB / ID: 5n2i | |||||||||
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Title | F420:NADPH oxidoreductase from Thermobifida fusca with NADP+ bound | |||||||||
Components | Reduced coenzyme F420:NADP oxidoreductase | |||||||||
Keywords | OXIDOREDUCTASE / F420:NADPH oxidoreductase / NADP+ bound / dimer of dimers | |||||||||
Function / homology | Function and homology information coenzyme F420 binding / Oxidoreductases; Acting on NADH or NADPH; With unknown physiological acceptors / NADPH regeneration / oxidoreductase activity, acting on NAD(P)H / NADP binding Similarity search - Function | |||||||||
Biological species | Thermobifida fusca (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | |||||||||
Authors | Kumar, H. / Nguyen, Q.-T. / Binda, C. / Mattevi, A. / Fraaije, M.W. | |||||||||
Funding support | Netherlands, 2items
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Citation | Journal: J. Biol. Chem. / Year: 2017 Title: Isolation and characterization of a thermostable F420:NADPH oxidoreductase from Thermobifida fusca. Authors: Kumar, H. / Nguyen, Q.T. / Binda, C. / Mattevi, A. / Fraaije, M.W. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5n2i.cif.gz | 193.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5n2i.ent.gz | 154.9 KB | Display | PDB format |
PDBx/mmJSON format | 5n2i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5n2i_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 5n2i_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 5n2i_validation.xml.gz | 41.8 KB | Display | |
Data in CIF | 5n2i_validation.cif.gz | 58.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n2/5n2i ftp://data.pdbj.org/pub/pdb/validation_reports/n2/5n2i | HTTPS FTP |
-Related structure data
Related structure data | 1jaxS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 24332.832 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: The residues that are not present in the coordinates have no clear electron density. They are thus disordered and not included in the final model. Source: (gene. exp.) Thermobifida fusca (strain YX) (bacteria) Strain: YX / Gene: Tfu_0970 / Production host: Escherichia coli (E. coli) References: UniProt: Q47RA9, Oxidoreductases; Acting on NADH or NADPH; With unknown physiological acceptors #2: Chemical | ChemComp-NAP / #3: Chemical | ChemComp-GOL / #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: 2.49 Å3/Da / Density % sol: 50.64 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG3000, PEG400, glycerol, HEPES pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9726 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 11, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9726 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→72.87 Å / Num. obs: 89383 / % possible obs: 98.6 % / Redundancy: 4.5 % / CC1/2: 0.994 / Rmerge(I) obs: 0.112 / Net I/σ(I): 7.9 |
Reflection shell | Resolution: 1.8→1.83 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.991 / Mean I/σ(I) obs: 0.9 / Num. unique all: 4183 / CC1/2: 0.247 / % possible all: 90.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1JAX Resolution: 1.8→72.86 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.949 / SU B: 3.626 / SU ML: 0.103 / Cross valid method: THROUGHOUT / ESU R: 0.111 / ESU R Free: 0.116 / 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: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.193 Å2
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Refinement step | Cycle: 1 / Resolution: 1.8→72.86 Å
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Refine LS restraints |
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