[English] 日本語
Yorodumi- PDB-4bpr: FERREDOXIN-NADP REDUCTASE MUTANT WITH TYR 79 REPLACED BY PHE (Y79F) -
+Open data
-Basic information
Entry | Database: PDB / ID: 4bpr | ||||||
---|---|---|---|---|---|---|---|
Title | FERREDOXIN-NADP REDUCTASE MUTANT WITH TYR 79 REPLACED BY PHE (Y79F) | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Herguedas, B. / Martinez-Julvez, M. / Sanchez-Azqueta, A. / Hervas, M. / Navarro, J.A. / Medina, M. | ||||||
Citation | Journal: Biochim.Biophys.Acta / Year: 2013 Title: A Hydrogen Bond Network in the Active Site of Anabaena Ferredoxin-Nadp(+) Reductase Modulates its Catalytic Efficiency. Authors: Sanchez-Azqueta, A. / Herguedas, B. / Hurtado-Guerrero, R. / Hervas, M. / Navarro, J.A. / Martinez-Julvez, M. / Medina, M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4bpr.cif.gz | 81.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4bpr.ent.gz | 58.6 KB | Display | PDB format |
PDBx/mmJSON format | 4bpr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bp/4bpr ftp://data.pdbj.org/pub/pdb/validation_reports/bp/4bpr | HTTPS FTP |
---|
-Related structure data
Related structure data | 3zbtC 3zbuC 3zc3C 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: 34025.676 Da / Num. of mol.: 1 / Fragment: RESIDUES 138-440 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ANABAENA SP. (bacteria) / Strain: PCC7119 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P21890, ferredoxin-NADP+ reductase |
---|---|
#2: Chemical | ChemComp-FAD / |
#3: Chemical | ChemComp-GOL / |
#4: Chemical | ChemComp-SO4 / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.86 Å3/Da / Density % sol: 57 % / Description: NONE |
---|---|
Crystal grow | Details: 18% PEG 6000, 0.1 M NAAC PH 5.5, 20 MM (NH4)2 SO4 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Wavelength: 1.54178 |
Detector | Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 2→25.67 Å / Num. obs: 24583 / % possible obs: 90.1 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Rmerge(I) obs: 0.08 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.3 / % possible all: 83.6 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1QUE Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.928 / SU B: 3.194 / SU ML: 0.091 / Cross valid method: THROUGHOUT / ESU R: 0.189 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.228 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→20 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|