[English] 日本語
Yorodumi- PDB-1qgz: FERREDOXIN:NADP+ REDUCTASE MUTANT WITH LEU 78 REPLACED BY ASP (L78D) -
+Open data
-Basic information
Entry | Database: PDB / ID: 1qgz | ||||||
---|---|---|---|---|---|---|---|
Title | FERREDOXIN:NADP+ REDUCTASE MUTANT WITH LEU 78 REPLACED BY ASP (L78D) | ||||||
Components | PROTEIN (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: 2.3 Å | ||||||
Authors | Hermoso, J.A. / Mayoral, T. / Medina, M. / Sanz-Aparicio, J. / Gomez-Moreno, C. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2001 Title: Role of a cluster of hydrophobic residues near the FAD cofactor in Anabaena PCC 7119 ferredoxin-NADP+ reductase for optimal complex formation and electron transfer to ferredoxin. Authors: Martinez-Julvez, M. / Nogues, I. / Faro, M. / Hurley, J.K. / Brodie, T.B. / Mayoral, T. / Sanz-Aparicio, J. / Hermoso, J.A. / Stankovich, M.T. / Medina, M. / Tollin, G. / 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1qgz.cif.gz | 81.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1qgz.ent.gz | 59 KB | Display | PDB format |
PDBx/mmJSON format | 1qgz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qg/1qgz ftp://data.pdbj.org/pub/pdb/validation_reports/qg/1qgz | HTTPS FTP |
---|
-Related structure data
Related structure data | 1h85C 1qh0C 1queS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 33204.637 Da / Num. of mol.: 1 / Mutation: L78D Source method: isolated from a genetically manipulated source Details: COMPLEXED WITH FLAVIN-ADENINE DINUCLEOTIDE / Source: (gene. exp.) Nostoc sp. (bacteria) / Strain: PCC 7119 / Production host: Escherichia coli (E. coli) / References: UniProt: P21890, ferredoxin-NADP+ reductase |
---|---|
#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 |
---|
-Sample preparation
Crystal | Density Matthews: 3 Å3/Da / Density % sol: 60 % | ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 5 / Details: pH 5.0 | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 8 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 291 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 1, 1998 |
Radiation | Monochromator: GRAPHITE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→35.57 Å / Num. obs: 18686 / % possible obs: 99.4 % / Observed criterion σ(I): 3 / Redundancy: 7.7 % / Rmerge(I) obs: 0.081 / Rsym value: 0.081 / Net I/σ(I): 8.2 |
Reflection shell | Resolution: 2.3→2.4 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.224 / Mean I/σ(I) obs: 3.4 / Rsym value: 0.224 / % possible all: 99.4 |
Reflection | *PLUS Lowest resolution: 35.6 Å |
Reflection shell | *PLUS % possible obs: 96 % |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1QUE Resolution: 2.3→7 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Cross valid method: FREE R / σ(F): 0
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→7 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.3→2.4 Å / Total num. of bins used: 8
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.843 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 7 % / Rfactor obs: 0.178 / Rfactor Rfree: 0.227 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.27 / % reflection Rfree: 7 % / Rfactor Rwork: 0.22 |