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Yorodumi- PDB-1sm4: Crystal Structure Analysis of the Ferredoxin-NADP+ Reductase from... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1sm4 | |||||||||
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Title | Crystal Structure Analysis of the Ferredoxin-NADP+ Reductase from Paprika | |||||||||
Components | chloroplast ferredoxin-NADP+ oxidoreductase | |||||||||
Keywords | OXIDOREDUCTASE / Rossmann fold | |||||||||
Function / homology | Function and homology information ferredoxin-NADP+ reductase / ferredoxin-NADP+ reductase activity / chloroplast / nucleotide binding Similarity search - Function | |||||||||
Biological species | Capsicum annuum (plant) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | |||||||||
Authors | Dorowski, A. / Hofmann, A. / Steegborn, C. / Boicu, M. / Huber, R. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2001 Title: Crystal structure of paprika ferredoxin-NADP+ reductase. Implications for the electron transfer pathway. Authors: Dorowski, A. / Hofmann, A. / Steegborn, C. / Boicu, M. / Huber, R. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1sm4.cif.gz | 141.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1sm4.ent.gz | 107.9 KB | Display | PDB format |
PDBx/mmJSON format | 1sm4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sm/1sm4 ftp://data.pdbj.org/pub/pdb/validation_reports/sm/1sm4 | HTTPS FTP |
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-Related structure data
Related structure data | 1fndS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 33428.336 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Capsicum annuum (plant) / Plasmid: PET22B(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9M4D2, ferredoxin-NADP+ reductase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.28 Å3/Da / Density % sol: 62.46 % | ||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion / Details: TRIS/HCL, AMMONIUM SULFATE, VAPOR DIFFUSION | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 8 / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→20 Å / Num. obs: 26895 / % possible obs: 83.9 % / Biso Wilson estimate: 15.1 Å2 / Rmerge(I) obs: 0.094 |
Reflection shell | Resolution: 2.5→2.58 Å / Rmerge(I) obs: 0.319 / % possible all: 83.5 |
Reflection | *PLUS Lowest resolution: 20 Å / Num. measured all: 61664 |
Reflection shell | *PLUS % possible obs: 83.5 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1FND, poly-Ala Resolution: 2.5→20 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1381854.36 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 98.2811 Å2 / ksol: 0.376474 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 8 Å / Num. reflection obs: 24312 / % reflection Rfree: 5 % / Rfactor Rfree: 0.265 / Rfactor Rwork: 0.198 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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