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Yorodumi- PDB-7sv0: NADPH-dependent cytochrome P450 reductase 2b from Sorghum bicolor... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7sv0 | |||||||||
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Title | NADPH-dependent cytochrome P450 reductase 2b from Sorghum bicolor (SbCPR2b) -oxidized form of NADP+ complex | |||||||||
Components | NADPH--cytochrome P450 reductase | |||||||||
Keywords | OXIDOREDUCTASE / NADPH-dependent cytochrome P450 reductase 2b from sorghum bicolor | |||||||||
Function / homology | Function and homology information NADPH-hemoprotein reductase / NADPH-hemoprotein reductase activity / FMN binding / flavin adenine dinucleotide binding / NADP binding / endoplasmic reticulum membrane / cytosol Similarity search - Function | |||||||||
Biological species | Sorghum bicolor (sorghum) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | |||||||||
Authors | Zhang, B. / Kang, C. | |||||||||
Funding support | United States, 2items
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Citation | Journal: J.Biol.Chem. / Year: 2022 Title: Functional and structural insight into the flexibility of cytochrome P450 reductases from Sorghum bicolor and its implications for lignin composition. Authors: Zhang, B. / Munske, G.R. / Timokhin, V.I. / Ralph, J. / Davydov, D.R. / Vermerris, W. / Sattler, S.E. / Kang, C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7sv0.cif.gz | 180.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7sv0.ent.gz | 140 KB | Display | PDB format |
PDBx/mmJSON format | 7sv0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sv/7sv0 ftp://data.pdbj.org/pub/pdb/validation_reports/sv/7sv0 | HTTPS FTP |
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-Related structure data
Related structure data | 7suxC 7suzC 5gxuS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 77553.031 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sorghum bicolor (sorghum) / Gene: CPR, SORBI_3007G088000 / Production host: Escherichia coli (E. coli) / References: UniProt: C5YJG8, NADPH-hemoprotein reductase |
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#2: Chemical | ChemComp-NAP / |
#3: Chemical | ChemComp-FAD / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.58 Å3/Da / Density % sol: 22.28 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / Details: 0.2 M sodium thiocyanate, pH 6.9, 20% w/v PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 26, 2021 |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→44.83 Å / Num. obs: 14106 / % possible obs: 99.82 % / Redundancy: 5.5 % / Biso Wilson estimate: 71.32 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.123 / Net I/σ(I): 10.18 |
Reflection shell | Resolution: 2.7→2.797 Å / Rmerge(I) obs: 1.537 / Num. unique obs: 1372 / CC1/2: 0.994 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 5GXU Resolution: 2.7→44.83 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 27.97 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 171.02 Å2 / Biso mean: 86.4804 Å2 / Biso min: 39.67 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.7→44.83 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10 / % reflection obs: 100 %
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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