+Open data
-Basic information
Entry | Database: PDB / ID: 4qtz | ||||||
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Title | Crystal Structure of Cinnamyl-Alcohol Dehydrogenase 2 | ||||||
Components | Dihydroflavonol-4-reductase | ||||||
Keywords | OXIDOREDUCTASE / dehydrogenase / monolignol / short-chain dehydrogenase/reductase / Rossmann fold | ||||||
Function / homology | Function and homology information cinnamoyl-CoA reductase / : / cinnamyl-alcohol dehydrogenase activity / phenylpropanoid biosynthetic process / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / cytoplasm Similarity search - Function | ||||||
Biological species | Medicago truncatula (barrel medic) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Pan, H. / Wang, X. | ||||||
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 | 4qtz.cif.gz | 80.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4qtz.ent.gz | 59.1 KB | Display | PDB format |
PDBx/mmJSON format | 4qtz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4qtz_validation.pdf.gz | 424 KB | Display | wwPDB validaton report |
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Full document | 4qtz_full_validation.pdf.gz | 428.8 KB | Display | |
Data in XML | 4qtz_validation.xml.gz | 16.4 KB | Display | |
Data in CIF | 4qtz_validation.cif.gz | 24.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qt/4qtz ftp://data.pdbj.org/pub/pdb/validation_reports/qt/4qtz | HTTPS FTP |
-Related structure data
Related structure data | 4qukC 4r1sC 4r1tC 4r1uC 2c29S C: citing same article (ref.) 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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Unit cell |
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-Components
#1: Protein | Mass: 35333.512 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Medicago truncatula (barrel medic) / Gene: MTR_3g005170 / Production host: Escherichia coli (E. coli) References: UniProt: G7IYC1, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor |
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#2: 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: 2.15 Å3/Da / Density % sol: 42.72 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion / pH: 6.5 Details: 25% PEG3350, 0.1 M Bis-Tris, pH 6.5, VAPOR DIFFUSION, temperature 277K |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 1, 2012 / Details: mirror |
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→25.96 Å / Num. all: 20860 / Num. obs: 20860 / % possible obs: 97 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 14.6 Å2 / Rmerge(I) obs: 0.096 / Net I/σ(I): 16.3 |
Reflection shell | Resolution: 2→2.13 Å / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 2.7 / % possible all: 92.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2C29 Resolution: 2→25.95 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 117174.16 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 49.3793 Å2 / ksol: 0.35 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→25.95 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
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Xplor file |
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