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Yorodumi- PDB-1bqe: FERREDOXIN:NADP+ REDUCTASE MUTANT WITH THR 155 REPLACED BY GLY (T155G) -
+Open data
-Basic information
Entry | Database: PDB / ID: 1bqe | ||||||
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Title | FERREDOXIN:NADP+ REDUCTASE MUTANT WITH THR 155 REPLACED BY GLY (T155G) | ||||||
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 | Nostoc sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.45 Å | ||||||
Authors | Hermoso, J.A. / Mayoral, T. / Medina, M. / Martinez-Ripoll, M. / Martinez-Julvez, M. / Sanz-Aparicio, J. / Gomez-Moreno, C. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2001 Title: Probing the determinants of coenzyme specificity in ferredoxin-NADP+ reductase by site-directed mutagenesis. Authors: Medina, M. / Luquita, A. / Tejero, J. / Hermoso, J. / Mayoral, T. / Sanz-Aparicio, J. / Grever, K. / Gomez-Moreno, C. #1: Journal: J.Mol.Biol. / Year: 1996 Title: X-Ray Structure of the Ferredoxin:Nadp+ Reductase from the Cyanobacterium Anabaena Pcc 7119 at 1.8 A Resolution, and Crystallographic Studies of Nadp+ Binding at 2.25 A Resolution Authors: Serre, L. / Vellieux, F.M. / Medina, M. / Gomez-Moreno, C. / Fontecilla-Camps, 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 | 1bqe.cif.gz | 81 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1bqe.ent.gz | 58.8 KB | Display | PDB format |
PDBx/mmJSON format | 1bqe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1bqe_validation.pdf.gz | 477.2 KB | Display | wwPDB validaton report |
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Full document | 1bqe_full_validation.pdf.gz | 483.5 KB | Display | |
Data in XML | 1bqe_validation.xml.gz | 8.7 KB | Display | |
Data in CIF | 1bqe_validation.cif.gz | 13.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bq/1bqe ftp://data.pdbj.org/pub/pdb/validation_reports/bq/1bqe | HTTPS FTP |
-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: 33158.656 Da / Num. of mol.: 1 / Mutation: T155G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Nostoc sp. (bacteria) / Strain: PCC 7119 / Production host: Escherichia coli (E. coli) / References: UniProt: P21890, ferredoxin-NADP+ reductase |
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#2: Chemical | ChemComp-SO4 / |
#3: Chemical | ChemComp-FAD / |
#4: Water | ChemComp-HOH / |
-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 5.0 | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 291 K |
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Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418 |
Detector | Type: MAR scanner 180 mm plate / Detector: IMAGE PLATE / Date: Feb 1, 1998 |
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: 2.45→40.13 Å / Num. obs: 15728 / % possible obs: 99.5 % / Observed criterion σ(I): 3 / Redundancy: 7.7 % / Rmerge(I) obs: 0.105 / Rsym value: 0.105 / Net I/σ(I): 6.3 |
Reflection shell | Resolution: 2.45→2.58 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 2.7 / Rsym value: 0.27 / % possible all: 99.5 |
Reflection | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 40.1 Å / Rmerge(I) obs: 0.1 |
Reflection shell | *PLUS % possible obs: 97.2 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1QUE Resolution: 2.45→9 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Cross valid method: FREE-R / σ(F): 0
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Displacement parameters | Biso mean: 19.84 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.45→9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.51 Å / Total num. of bins used: 8
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Software | *PLUS Name: X-PLOR / Version: 3.843 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.4 Å / σ(F): 0 / % reflection Rfree: 7 % / Rfactor obs: 0.16 / Rfactor Rfree: 0.24 / Rfactor Rwork: 0.16 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2.4 Å / Rfactor Rfree: 0.3 / % reflection Rfree: 12.5 % / Rfactor Rwork: 0.21 |