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Yorodumi- PDB-2x3u: Ferredoxin-NADP reductase mutant with Tyr 303 replaced by Phe (Y303F) -
+Open data
-Basic information
Entry | Database: PDB / ID: 2x3u | ||||||
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Title | Ferredoxin-NADP reductase mutant with Tyr 303 replaced by Phe (Y303F) | ||||||
Components | FERREDOXIN-NADP REDUCTASEFerredoxin—NADP(+) reductase | ||||||
Keywords | OXIDOREDUCTASE / FLAVOPROTEIN | ||||||
Function / homology | Function and homology information ferredoxin-NADP+ reductase / ferredoxin-NADP+ reductase activity / phycobilisome / plasma membrane-derived thylakoid membrane / electron transport chain / NADP binding / flavin adenine dinucleotide binding Similarity search - Function | ||||||
Biological species | ANABAENA SP. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å | ||||||
Authors | Herguedas, B. / Martinez-Julvez, M. / Hermoso, J.A. / Peregrina, J.R. / Sanchez-Azqueta, A. / Medina, M. | ||||||
Citation | Journal: Biochim.Biophys.Acta / Year: 2010 Title: Role of Specific Residues in Coenzyme Binding, Charge-Transfer Complex Formation, and Catalysis in Anabaena Ferredoxin Nadp(+)-Reductase. Authors: Peregrina, J.R. / Sanchez-Azqueta, A. / Herguedas, B. / Martinez-Julvez, M. / Medina, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2x3u.cif.gz | 85.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2x3u.ent.gz | 62.8 KB | Display | PDB format |
PDBx/mmJSON format | 2x3u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x3/2x3u ftp://data.pdbj.org/pub/pdb/validation_reports/x3/2x3u | HTTPS FTP |
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-Related structure data
Related structure data | 1queS 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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Unit cell |
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-Components
#1: Protein | Mass: 34026.660 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ANABAENA SP. (bacteria) / Strain: PCC7119 / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P21890, ferredoxin-NADP+ reductase |
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#2: Chemical | ChemComp-FAD / |
#3: Chemical | ChemComp-SO4 / |
#4: Chemical | ChemComp-GOL / |
#5: Water | ChemComp-HOH / |
Compound details | ENGINEERED |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.97 Å3/Da / Density % sol: 58.57 % / Description: NONE |
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Crystal grow | Details: 18 % PEG 6000, 0.1 M NAAC PH 5.5, 20 MM (NH4)2SO4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM16 / Wavelength: 0.97918 |
Detector | Date: Jun 29, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 1.93→74.44 Å / Num. obs: 28671 / % possible obs: 93.9 % / Observed criterion σ(I): 3 / Redundancy: 6 % / Rmerge(I) obs: 0.08 |
Reflection shell | Resolution: 1.93→2.01 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.3 / % possible all: 88.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1QUE Resolution: 1.93→37.35 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.932 / SU B: 2.819 / SU ML: 0.083 / Cross valid method: THROUGHOUT / ESU R: 0.151 / ESU R Free: 0.135 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.542 Å2
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Refinement step | Cycle: LAST / Resolution: 1.93→37.35 Å
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Refine LS restraints |
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