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Yorodumi- PDB-1quf: X-RAY STRUCTURE OF A COMPLEX NADP+-FERREDOXIN:NADP+ REDUCTASE FRO... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1quf | ||||||
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Title | X-RAY STRUCTURE OF A COMPLEX NADP+-FERREDOXIN:NADP+ REDUCTASE FROM THE CYANOBACTERIUM ANABAENA PCC 7119 AT 2.25 ANGSTROMS | ||||||
Components | FERREDOXIN-NADP+ REDUCTASEFerredoxin—NADP(+) reductase | ||||||
Keywords | OXIDOREDUCTASE / FLAVOPROTEIN / NADP / FAD / THYLAKOID MEMBRANE / HYCOBILISOME / 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 / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | ||||||
Authors | Serre, L. / Frey, M. / Vellieux, F.M.D. | ||||||
Citation | 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. #1: Journal: J.Mol.Biol. / Year: 1991 Title: Crystals of Anabaena Pcc 7119 Ferredoxin-Nadp+ Reductase Authors: Serre, L. / Medina, M. / Gomez-Moreno, C. / Fontecilla-Camps, J.C. / Frey, M. #2: Journal: Nucleic Acids Res. / Year: 1990 Title: Sequence of the Ferredoxin-Nadp(+)-Reductase Gene from Anabaena Pcc 7119 Authors: Fillat, M.F. / Bakker, H.A. / Weisbeek, P.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1quf.cif.gz | 84.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1quf.ent.gz | 62.6 KB | Display | PDB format |
PDBx/mmJSON format | 1quf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qu/1quf ftp://data.pdbj.org/pub/pdb/validation_reports/qu/1quf | HTTPS FTP |
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-Related 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: 34173.855 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nostoc sp. (bacteria) / Strain: PCC 7119 / References: UniProt: P21890, ferredoxin-NADP+ reductase |
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#2: Chemical | ChemComp-FAD / |
#3: Chemical | ChemComp-NAP / |
#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: 5.5 / Details: SEE REFERENCE 1., pH 5.5 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: May 1, 1996 |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→20 Å / Num. obs: 15544 / % possible obs: 83 % / Observed criterion σ(I): 2 / Redundancy: 3 % / Rsym value: 0.735 |
Reflection shell | Resolution: 2.25→2.34 Å / Redundancy: 2 % / % possible all: 34 |
Reflection | *PLUS Num. measured all: 48735 / Rmerge(I) obs: 0.0735 |
Reflection shell | *PLUS % possible obs: 34 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: ANABAENA NATIVE FNR X-RAY MODEL AT 1.8 ANGSTROMS Resolution: 2.25→15 Å / σ(F): 3
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Displacement parameters | Biso mean: 14.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.25→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.25→2.42 Å
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Xplor file |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor obs: 0.24 |