+Open data
-Basic information
Entry | Database: PDB / ID: 4r1u | ||||||
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Title | Crystal structure of Medicago truncatula cinnamoyl-CoA reductase | ||||||
Components | Cinnamoyl CoA reductase | ||||||
Keywords | OXIDOREDUCTASE / cinnamoyl-CoA reductase / short-chain dehydrogenase/reductase | ||||||
Function / homology | Function and homology information cinnamoyl-CoA reductase activity / cinnamoyl-CoA reductase / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / oxidoreductase activity Similarity search - Function | ||||||
Biological species | Medicago truncatula (barrel medic) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.18 Å | ||||||
Authors | Noel, J.P. / Bomati, E.K. / Louie, G.V. / Bowman, M.E. | ||||||
Citation | Journal: Plant Cell / Year: 2014 Title: Structural Studies of Cinnamoyl-CoA Reductase and Cinnamyl-Alcohol Dehydrogenase, Key Enzymes of Monolignol Biosynthesis. Authors: Pan, H. / Zhou, R. / Louie, G.V. / Muhlemann, J.K. / Bomati, E.K. / Bowman, M.E. / Dudareva, N. / Dixon, R.A. / Noel, J.P. / Wang, X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4r1u.cif.gz | 137.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4r1u.ent.gz | 108 KB | Display | PDB format |
PDBx/mmJSON format | 4r1u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r1/4r1u ftp://data.pdbj.org/pub/pdb/validation_reports/r1/4r1u | HTTPS FTP |
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-Related 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: 38603.660 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Medicago truncatula (barrel medic) / Gene: MtCCR2, MTR_4g006940 / Plasmid: pHIS8 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: G7JEE5 #2: Chemical | #3: 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: 2.46 Å3/Da / Density % sol: 49.99 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 21% (w/v) polyethylene glycol 8000, 0.2 M potassium acetate, 100 mM HEPES, and 2 mM DTT, pH 7.5, vapor diffusion, hanging drop, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9792, 0.9184, 0.9794 | ||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Details: mirrors | ||||||||||||
Radiation | Monochromator: double crystal Si(111) / Protocol: MAD / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Highest resolution: 2.18 Å / Num. all: 38353 / Num. obs: 38353 |
-Phasing
Phasing | Method: MAD |
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-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.18→19.98 Å / FOM work R set: 0.781 / SU ML: 0.28 / σ(F): 0.49 / Phase error: 28.05 / 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: 98.69 Å2 / Biso mean: 37.13 Å2 / Biso min: 14.58 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.18→19.98 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 27
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