+Open data
-Basic information
Entry | Database: PDB / ID: 1b2r | ||||||
---|---|---|---|---|---|---|---|
Title | FERREDOXIN-NADP+ REDUCTASE (MUTATION: E 301 A) | ||||||
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 / phycobilisome / plasma membrane-derived thylakoid membrane / electron transport chain / flavin adenine dinucleotide binding / NADP binding Similarity search - Function | ||||||
Biological species | Nostoc sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Hermoso, J.A. / Mayoral, T. / Medina, M. / Martinez-Ripoll, M. / Martinez-Julvez, M. / Sanz-Aparicio, J. / Gomez-Moreno, C. | ||||||
Citation | Journal: Proteins / Year: 2000 Title: Structural basis of the catalytic role of Glu301 in Anabaena PCC 7119 ferredoxin-NADP+ reductase revealed by x-ray crystallography. Authors: Mayoral, T. / Medina, M. / Sanz-Aparicio, J. / Gomez-Moreno, C. / Hermoso, J.A. #1: Journal: J.Mol.Biol. / Year: 1996 Title: X-Ray Structure of the Ferredoxin:NADP+ Reductase from the Cyanobacterium Anabanena PCC 7119 at 1.8 Angstroms Resolution, and Crystallographic Studies of NADP+ Binding at 2.25 Angstroms 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 | 1b2r.cif.gz | 91.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1b2r.ent.gz | 65.9 KB | Display | PDB format |
PDBx/mmJSON format | 1b2r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b2/1b2r ftp://data.pdbj.org/pub/pdb/validation_reports/b2/1b2r | 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: 34114.836 Da / Num. of mol.: 1 / Mutation: E301A 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 |
---|---|
#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: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM02 / Wavelength: 1.01 |
Detector | Detector: CCD / Date: Feb 15, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.01 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→37.5 Å / Num. obs: 38021 / % possible obs: 98.6 % / Observed criterion σ(I): 3 / Redundancy: 5.2 % / Rmerge(I) obs: 0.067 / Rsym value: 0.067 / Net I/σ(I): 8.1 |
Reflection shell | Resolution: 1.81→1.93 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.072 / Mean I/σ(I) obs: 10.3 / Rsym value: 0.072 / % possible all: 91.8 |
Reflection shell | *PLUS % possible obs: 91.8 % |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1QUE Resolution: 1.8→7 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Cross valid method: FREE-R / σ(F): 0
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→7 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.8→1.88 Å / Total num. of bins used: 8
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.843 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 7 Å / σ(F): 0 / % reflection Rfree: 7 % / Rfactor obs: 0.19 / Rfactor Rfree: 0.24 / Rfactor Rwork: 0.19 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 23.2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Highest resolution: 1.8 Å / Rfactor Rfree: 0.257 / % reflection Rfree: 7.8 % / Rfactor Rwork: 0.237 / Rfactor obs: 0.237 |