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Yorodumi- PDB-3zbu: Ferredoxin-NADP Reductase Mutant with SER 80 Replaced by ALA (S80A) -
+Open data
-Basic information
Entry | Database: PDB / ID: 3zbu | ||||||
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Title | Ferredoxin-NADP Reductase Mutant with SER 80 Replaced by ALA (S80A) | ||||||
Components | FERREDOXIN-NADP REDUCTASEFerredoxin—NADP(+) reductase | ||||||
Keywords | OXIDOREDUCTASE | ||||||
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. PCC7119 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.89 Å | ||||||
Authors | Martinez-Julvez, M. / Herguedas, B. / 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3zbu.cif.gz | 83.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zbu.ent.gz | 60.6 KB | Display | PDB format |
PDBx/mmJSON format | 3zbu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zb/3zbu ftp://data.pdbj.org/pub/pdb/validation_reports/zb/3zbu | HTTPS FTP |
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-Related structure data
Related structure data | 3zbtC 3zc3C 4bprC 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: 34027.645 Da / Num. of mol.: 1 / Fragment: RESIDUES 138-440 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) NOSTOC SP. PCC7119 (bacteria) / 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-GOL / #4: Chemical | ChemComp-SO4 / | #5: 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: 2.68 Å3/Da / Density % sol: 53.7 % / Description: NONE |
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Crystal grow | Details: 18 % PEG 6000, 0.1 M NAAC PH 5.5, 20 MM (NH4)2SO4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER-INCOATEC MICROFOCUS / Wavelength: 1.54178 |
Detector | Type: BRUKER AXIOM / Detector: CCD / Date: Jul 14, 2010 |
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→59.53 Å / Num. obs: 30565 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 4.74 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 17.05 |
Reflection shell | Resolution: 1.9→1.99 Å / Redundancy: 3.48 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 3.67 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1QUE Resolution: 1.89→75.38 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.929 / SU B: 2.46 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.132 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 105-111 ARE DISORDERED.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.137 Å2
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Refinement step | Cycle: LAST / Resolution: 1.89→75.38 Å
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