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Yorodumi- PDB-2vyq: FERREDOXIN:NADP REDUCTASE MUTANT WITH THR 155 REPLACED BY GLY, AL... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2vyq | ||||||
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Title | FERREDOXIN:NADP REDUCTASE MUTANT WITH THR 155 REPLACED BY GLY, ALA 160 REPLACED BY THR, LEU 263 REPLACED BY PRO AND TYR 303 REPLACED BY SER (T155G-A160T-L263P-Y303S) | ||||||
Components | FERREDOXIN-NADP REDUCTASEFerredoxin—NADP(+) reductase | ||||||
Keywords | OXIDOREDUCTASE / PHYCOBILISOME / FAD / NADP / MEMBRANE / THYLAKOID / 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 | NOSTOC SP. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Herguedas, B. / Martinez-Julvez, M. / Hermoso, J.A. / Peregrina, J.R. / Medina, M. | ||||||
Citation | Journal: Biochemistry / Year: 2009 Title: Protein Motifs Involved in Coenzyme Interaction and Enzymatic Efficiency in Anabaena Ferredoxin-Nadp+ Reductase. Authors: Peregrina, J.R. / Herguedas, B. / Hermoso, J.A. / Martinez-Julvez, M. / Medina, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2vyq.cif.gz | 87.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vyq.ent.gz | 64.1 KB | Display | PDB format |
PDBx/mmJSON format | 2vyq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vy/2vyq ftp://data.pdbj.org/pub/pdb/validation_reports/vy/2vyq | HTTPS FTP |
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-Related structure data
Related structure data | 2bmwC 2vzlC 1queS C: citing same article (ref.) S: Starting model for refinement |
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Similar 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: 34067.691 Da / Num. of mol.: 1 / Fragment: RESIDUES 137-440 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) NOSTOC SP. (bacteria) / Strain: PCC 7119 / Plasmid: PET 28B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P21890, ferredoxin-NADP+ reductase | ||||||
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#2: Chemical | ChemComp-FAD / | ||||||
#3: Chemical | ChemComp-SO4 / | ||||||
#4: Chemical | #5: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN A, THR 292 TO GLY ENGINEERED RESIDUE IN CHAIN A, ALA 297 TO THR ...ENGINEERED | Sequence details | FNR MUTANT (T155G, A160T, L263P, Y303S) | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.85 Å3/Da / Density % sol: 56.9 % / Description: NONE |
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Crystal grow | pH: 5.5 Details: 18-20 % (W/V) PEG 6000 20 MM AMMONIUM SULPHATE 0.1M MES/NAOH, PH 5.0-5.5 B-OCTYL GLYCOSIDE AT 2%(W/V) |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54178 |
Detector | Type: BRUKER-NONIUS / Detector: CCD / Date: Jun 30, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→75.38 Å / Num. obs: 30845 / % possible obs: 99.1 % / Observed criterion σ(I): 2 / Redundancy: 5.26 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 23.85 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 2.54 % / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 5.45 / % possible all: 93.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1QUE Resolution: 1.9→19.8 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.935 / SU B: 2.282 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.124 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES N237, M266 AND E301 PRESENTED DOUBLE CONFORMATION. OCCUPANCIES 0.5
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.18 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→19.8 Å
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Refine LS restraints |
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