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Yorodumi- PDB-1ogi: FERREDOXIN:NADP+ REDUCTASE MUTANT WITH THR 155 REPLACED BY GLY AN... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ogi | ||||||
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Title | FERREDOXIN:NADP+ REDUCTASE MUTANT WITH THR 155 REPLACED BY GLY AND ALA 160 REPLACED BY THR (T155G-A160T) | ||||||
Components | FERREDOXIN--NADP+ REDUCTASE | ||||||
Keywords | OXIDOREDUCTASE / FLAVOPROTEIN / NADP / FAD / FNR / NADP REDUCTASE | ||||||
Function / homology | Function and homology information ferredoxin-NADP+ reductase / ferredoxin-NADP+ reductase activity / NADPH dehydrogenase 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 / MOLECULAR REPLACEMENT / Resolution: 1.64 Å | ||||||
Authors | Hermoso, J.A. / Mayoral, T. / Julvez, M.M. / Medina, M. / Sanz-Aparicio, J. / Gomez-Moreno, C. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2003 Title: Involvement of the Pyrophosphate and the 2'-Phosphate Binding Regions of Ferredoxin-Nadp+ Reductase in Coenzyme Specificity. Authors: Tejero, J. / Martinez-Julvez, M. / Mayoral, T. / Luquita, A. / Sanz-Aparicio, J. / Hermoso, J.A. / Hurley, J.K. / Tollin, G. / Gomez-Moreno, C. / Medina, M. #1: Journal: J.Mol.Biol. / Year: 1996 Title: X-Ray Structure of the Ferredoxin:Nadp+ Reductase from the Cyanobacterium Anabanena Pcc 7119 at 1.8A Resolution,Band Crystallographic Studies of Nadp Binding at 2.25A Resolution Authors: Serre, L. / Vellieux, F.M.D. / Medina, M. / Gomez-Moreno, C. / Fontecilla, J.C. / Frey, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ogi.cif.gz | 83.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ogi.ent.gz | 60.4 KB | Display | PDB format |
PDBx/mmJSON format | 1ogi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/og/1ogi ftp://data.pdbj.org/pub/pdb/validation_reports/og/1ogi | HTTPS FTP |
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-Related structure data
Related structure data | 1h42C 1ogjC 1queS C: citing same article (ref.) 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: 34027.648 Da / Num. of mol.: 1 / Fragment: RESIDUES 138-440 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ANABAENA SP. (STRAIN PCC 7119) (bacteria) Strain: PCC 7119 / 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: Water | ChemComp-HOH / |
Compound details | CHAIN A ENGINEERED |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3 Å3/Da / Density % sol: 60 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 5 / Details: pH 5.00 | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 8 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418 |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 15, 2002 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.64→20.49 Å / Num. obs: 50902 / % possible obs: 98.9 % / Observed criterion σ(I): 3 / Redundancy: 12.7 % / Biso Wilson estimate: 24.1 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 0.067 |
Reflection shell | Resolution: 1.64→1.73 Å / Redundancy: 11.3 % / Rmerge(I) obs: 0.71 / Mean I/σ(I) obs: 0.71 / % possible all: 98.9 |
Reflection | *PLUS Highest resolution: 1.63 Å / Lowest resolution: 20.49 Å / Rmerge(I) obs: 0.067 |
Reflection shell | *PLUS Highest resolution: 1.63 Å / % possible obs: 98.9 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1QUE Resolution: 1.64→20.5 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1405773.7 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 22.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.64→20.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.64→1.74 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
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Refinement | *PLUS Highest resolution: 1.6 Å / Lowest resolution: 20.5 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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