[English] 日本語
Yorodumi- PDB-1gr1: Structure of Ferredoxin-NADP+ Reductase with Glu 139 replaced by ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1gr1 | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of Ferredoxin-NADP+ Reductase with Glu 139 replaced by Lys (E139K) | ||||||
Components | FERREDOXIN--NADP+ REDUCTASE | ||||||
Keywords | OXIDOREDUCTASE / FLAVOPROTEIN / 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. PCC7119 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Hermoso, J.A. / Mayoral, T. / Medina, M. / Sanz-Aparicio, J. / Gomez-Moreno, C. | ||||||
Citation | Journal: Eur.J.Biochem. / Year: 2002 Title: Probing the Role of Glutamic Acid 139 of Anabena Ferrodoxin-Nadp+ Reductase in the Interaction with Substrates Authors: Faro, M. / Frago, S. / Mayoral, T. / Hermoso, J.A. / Sanz-Aparico, J. / 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, and 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1gr1.cif.gz | 79.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1gr1.ent.gz | 57.8 KB | Display | PDB format |
PDBx/mmJSON format | 1gr1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gr/1gr1 ftp://data.pdbj.org/pub/pdb/validation_reports/gr/1gr1 | HTTPS FTP |
---|
-Related structure data
Related structure data | 1queS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 34041.742 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) NOSTOC SP. PCC7119 (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P21890, ferredoxin-NADP+ reductase |
---|---|
#2: Chemical | ChemComp-FAD / |
#3: Chemical | ChemComp-SO4 / |
#4: Water | ChemComp-HOH / |
Compound details | ENGINEERED |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.3 Å3/Da / Density % sol: 63 % | ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 5.5 / Details: pH 5.50 | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20-23 ℃ / pH: 8 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 15, 2001 |
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: 2.5→27.3 Å / Num. obs: 13944 / % possible obs: 97.1 % / Observed criterion σ(I): 3 / Redundancy: 3.9 % / Rmerge(I) obs: 0.167 / Net I/σ(I): 3.2 |
Reflection shell | Resolution: 2.5→2.64 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.264 / Mean I/σ(I) obs: 2.6 / % possible all: 99.9 |
Reflection shell | *PLUS % possible obs: 99.9 % |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1QUE Resolution: 2.5→10 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Cross valid method: FREE R-VALUE / σ(F): 0 / Details: NO ELECTRON DENSITY PRESENT FOR RESIDUES 1-8
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.15 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→10 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.5→2.61 Å / Total num. of bins used: 8
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 10 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|