+Open data
-Basic information
Entry | Database: PDB / ID: 7tvw | ||||||
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Title | Crystal structure of Arabidopsis thaliana DLK2 | ||||||
Components | Alpha/beta-Hydrolases superfamily protein | ||||||
Keywords | HYDROLASE / Sesquiterpene lactone perception | ||||||
Function / homology | alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold / hydrolase activity / nucleus / cytoplasm / Alpha/beta-Hydrolases superfamily protein Function and homology information | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.48 Å | ||||||
Authors | Burger, M. / Chory, J. | ||||||
Funding support | 1items
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Citation | Journal: Plant Direct / Year: 2022 Title: Crystal structure of Arabidopsis DWARF14-LIKE2 (DLK2) reveals a distinct substrate binding pocket architecture. Authors: Burger, M. / Honda, K. / Kondoh, Y. / Hong, S. / Watanabe, N. / Osada, H. / Chory, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7tvw.cif.gz | 75.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7tvw.ent.gz | 52.5 KB | Display | PDB format |
PDBx/mmJSON format | 7tvw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7tvw_validation.pdf.gz | 421.3 KB | Display | wwPDB validaton report |
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Full document | 7tvw_full_validation.pdf.gz | 422.7 KB | Display | |
Data in XML | 7tvw_validation.xml.gz | 14.7 KB | Display | |
Data in CIF | 7tvw_validation.cif.gz | 22.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tv/7tvw ftp://data.pdbj.org/pub/pdb/validation_reports/tv/7tvw | HTTPS FTP |
-Related structure data
Related structure data | 4ih1S S: Starting model for refinement |
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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: 30207.766 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At3g24420 / Plasmid: pGEX4T3 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9LK01 |
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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: 2.14 Å3/Da / Density % sol: 42.55 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Tris, 1.9 M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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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: Apr 13, 2017 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.48→42.295 Å / Num. obs: 43371 / % possible obs: 99.7 % / Redundancy: 7.5 % / Biso Wilson estimate: 14.65 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.07077 / Net I/σ(I): 17.42 |
Reflection shell | Resolution: 1.48→1.533 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.7296 / Num. unique obs: 4281 / CC1/2: 0.881 / CC star: 0.968 / % possible all: 99.35 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4IH1 Resolution: 1.48→42.295 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.22 / 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: 103.46 Å2 / Biso mean: 20.8821 Å2 / Biso min: 6.43 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.48→42.295 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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