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Yorodumi- PDB-5tqm: Cinnamoyl-CoA Reductase 1 from Sorghum bicolor in complex with NADP+ -
+Open data
-Basic information
Entry | Database: PDB / ID: 5tqm | ||||||
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Title | Cinnamoyl-CoA Reductase 1 from Sorghum bicolor in complex with NADP+ | ||||||
Components | Cinnamoyl-CoA Reductase | ||||||
Keywords | OXIDOREDUCTASE / cinnamoyl-CoA reductase / CCR | ||||||
Function / homology | Function and homology information oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / nucleotide binding Similarity search - Function | ||||||
Biological species | Sorghum bicolor (sorghum) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Sattler, S.A. / Kang, C.H. | ||||||
Citation | Journal: Plant Physiol. / Year: 2017 Title: Structural and Biochemical Characterization of Cinnamoyl-CoA Reductases. Authors: Sattler, S.A. / Walker, A.M. / 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 | 5tqm.cif.gz | 239.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5tqm.ent.gz | 196 KB | Display | PDB format |
PDBx/mmJSON format | 5tqm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tq/5tqm ftp://data.pdbj.org/pub/pdb/validation_reports/tq/5tqm | HTTPS FTP |
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-Related structure data
Related structure data | 4r1sS 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: 41106.469 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sorghum bicolor (sorghum) / Gene: SORBI_007G141200 / Production host: Escherichia coli (E. coli) / References: UniProt: C5YLL4 #2: Chemical | #3: Chemical | #4: Chemical | |
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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: 2.25 Å3/Da / Density % sol: 45.44 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Bis-tris pH (6.5), 25% (w/v) PEG 3,350 |
-Data collection
Diffraction | Mean temperature: 80 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 23, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→50 Å / Num. obs: 19803 / % possible obs: 99.8 % / Redundancy: 5.2 % / Rsym value: 0.155 / Net I/σ(I): 24.234 |
Reflection shell | Resolution: 2.7→2.75 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 1.511 / Num. unique obs: 953 / Rsym value: 0.767 / % possible all: 97 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4R1S Resolution: 2.9→41.018 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 38.38 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→41.018 Å
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Refine LS restraints |
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LS refinement shell |
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