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Yorodumi- PDB-1jb9: Crystal Structure of The Ferredoxin:NADP+ Reductase From Maize Ro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1jb9 | ||||||
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Title | Crystal Structure of The Ferredoxin:NADP+ Reductase From Maize Root AT 1.7 Angstroms | ||||||
Components | ferredoxin-NADP reductase | ||||||
Keywords | OXIDOREDUCTASE / ELECTRON TRANSPORT | ||||||
Function / homology | Function and homology information oxidoreductase activity, acting on NAD(P)H, heme protein as acceptor / ferredoxin-NADP+ reductase / ferredoxin-NADP+ reductase activity / NADPH dehydrogenase activity / NADPH binding / photosynthesis / electron transport chain / electron transfer activity Similarity search - Function | ||||||
Biological species | Zea mays (maize) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Faber, H.R. / Karplus, P.A. / Aliverti, A. / Ferioli, C. / Spinola, M. | ||||||
Citation | Journal: Biochemistry / Year: 2001 Title: Biochemical and crystallographic characterization of ferredoxin-NADP(+) reductase from nonphotosynthetic tissues. Authors: Aliverti, A. / Faber, R. / Finnerty, C.M. / Ferioli, C. / Pandini, V. / Negri, A. / Karplus, P.A. / Zanetti, G. #1: Journal: FLAVINS AND FLAVOPROTEINS / Year: 1999 Title: Structural and Functional Properties of Corn Root Ferredoxin:NADP+ Reductase Authors: Aliverti, A. / Ferioli, C. / Spinola, M. / Raimondi, D. / Zanetti, G. / Finnerty, C. / Faber, R. / Karplus, P.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jb9.cif.gz | 81.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jb9.ent.gz | 59.1 KB | Display | PDB format |
PDBx/mmJSON format | 1jb9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1jb9_validation.pdf.gz | 721.7 KB | Display | wwPDB validaton report |
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Full document | 1jb9_full_validation.pdf.gz | 728.1 KB | Display | |
Data in XML | 1jb9_validation.xml.gz | 17 KB | Display | |
Data in CIF | 1jb9_validation.cif.gz | 25.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jb/1jb9 ftp://data.pdbj.org/pub/pdb/validation_reports/jb/1jb9 | HTTPS FTP |
-Related structure data
Related structure data | 3lvbC 1fnbS S: Starting model for refinement C: citing same article (ref.) |
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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: 35361.996 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Zea mays (maize) / Production host: Escherichia coli (E. coli) / References: UniProt: Q41736, ferredoxin-NADP+ reductase |
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#2: Chemical | ChemComp-FAD / |
#3: 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: 2.75 Å3/Da / Density % sol: 55.21 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: Peg 8000, Na Cacodylate, Mg Acetate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7 | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 1, 2000 / Details: Yale Mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→50 Å / Num. all: 47556 / Num. obs: 47556 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 1.7→50 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.294 / Mean I/σ(I) obs: 3 / % possible all: 96.1 |
Reflection | *PLUS Highest resolution: 1.7 Å / Lowest resolution: 50 Å / Num. obs: 43654 / % possible obs: 99.1 % / Num. measured all: 246386 / Rmerge(I) obs: 0.068 |
Reflection shell | *PLUS % possible obs: 97.6 % / Rmerge(I) obs: 0.364 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Modified 1FNB Resolution: 1.7→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 227.851 Å2 / ksol: 0.78246 e/Å3 | |||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.7→50 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Classification: refinement | |||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.7 Å / Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor all: 0.167 / Rfactor obs: 0.164 / Rfactor Rfree: 0.223 | |||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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