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Yorodumi- PDB-4b4d: Crystal structure of FAD-containing ferredoxin-NADP reductase fro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4b4d | ||||||
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Title | Crystal structure of FAD-containing ferredoxin-NADP reductase from Xanthomonas axonopodis pv. citri | ||||||
Components | FERREDOXIN-NADP REDUCTASEFerredoxin—NADP(+) reductase | ||||||
Keywords | OXIDOREDUCTASE | ||||||
Function / homology | Function and homology information ferredoxin-NADP+ reductase / ferredoxin-NADP+ reductase activity / nucleotide binding Similarity search - Function | ||||||
Biological species | XANTHOMONAS AXONOPODIS PV. CITRI STR. 306 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Martinez-Julvez, M. / Orellano, E.G. / Tondo, M.L. / Hurtado-Guerrero, R. / Medina, M. / Ceccarelli, E.A. / Sanchez-Azqueta, A. | ||||||
Citation | Journal: Biomed Res Int / Year: 2013 Title: Crystal Structure of Fad-Containing Ferredoxin- Nadp Reductase from Xanthomonas Axonopodis Pv. Citri Authors: Tondo, M.L. / Hurtado-Guerrero, R. / Sanchez-Azqueta, A. / Ceccarelli, E.A. / Medina, M. / Orellano, E.G. / Martinez-Julvez, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4b4d.cif.gz | 72.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4b4d.ent.gz | 52.1 KB | Display | PDB format |
PDBx/mmJSON format | 4b4d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b4/4b4d ftp://data.pdbj.org/pub/pdb/validation_reports/b4/4b4d | HTTPS FTP |
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-Related structure data
Related structure data | 2bgjS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 29787.807 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) XANTHOMONAS AXONOPODIS PV. CITRI STR. 306 (bacteria) Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYS / References: UniProt: Q8PMH0, ferredoxin-NADP+ reductase |
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#2: Chemical | ChemComp-FAD / |
#3: Chemical | ChemComp-CL / |
#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: 2.58 Å3/Da / Density % sol: 52.3 % / Description: NONE |
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Crystal grow | pH: 7.5 / Details: 4.3 M NACL AND 100 MM HEPES PH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM16 / Wavelength: 0.99994 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Sep 2, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99994 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→24.06 Å / Num. obs: 46901 / % possible obs: 96.7 % / Observed criterion σ(I): 2 / Redundancy: 4.6 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.7 |
Reflection shell | Resolution: 1.5→1.58 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 1.9 / % possible all: 79.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2BGJ Resolution: 1.5→76.4 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.947 / SU B: 1.627 / SU ML: 0.06 / Cross valid method: THROUGHOUT / ESU R: 0.085 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 1-3 RESIDUES HAVE NOT BEEN MODELED BECAUSE THEY ARE NOT DEFINED IN THE ELECTRON DENSITY
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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: 21.601 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→76.4 Å
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Refine LS restraints |
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