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- PDB-5zhr: Crystal structure of OsD14 in complex with covalently bound KK094 -
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Open data
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Basic information
Entry | Database: PDB / ID: 5zhr | ||||||||||||
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Title | Crystal structure of OsD14 in complex with covalently bound KK094 | ||||||||||||
![]() | Strigolactone esterase D14 | ||||||||||||
![]() | HYDROLASE / Plant hormones / Plant signalling / Strigolactones / receptor | ||||||||||||
Function / homology | ![]() strigolactone biosynthetic process / secondary shoot formation / Hydrolases; Acting on ester bonds / hydrolase activity / nucleus / cytoplasm Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Hirabayashi, K. / Miyakawa, T. / Tanokura, M. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Triazole Ureas Covalently Bind to Strigolactone Receptor and Antagonize Strigolactone Responses. Authors: Nakamura, H. / Hirabayashi, K. / Miyakawa, T. / Kikuzato, K. / Hu, W. / Xu, Y. / Jiang, K. / Takahashi, I. / Niiyama, R. / Dohmae, N. / Tanokura, M. / Asami, T. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 128 KB | Display | ![]() |
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PDB format | ![]() | 96.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1003.8 KB | Display | ![]() |
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Full document | ![]() | 1003.9 KB | Display | |
Data in XML | ![]() | 24.7 KB | Display | |
Data in CIF | ![]() | 37.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5zhsC ![]() 5zhtC ![]() 3vxkS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 30024.361 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: D14, D88, HTD2, Os03g0203200, LOC_Os03g10620 / Production host: ![]() ![]() References: UniProt: Q10QA5, Hydrolases; Acting on ester bonds #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.14 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: PEG 20000, MES |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jun 23, 2016 |
Radiation | Monochromator: Cryo-cooled channel-cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→49.511 Å / Num. obs: 173170 / % possible obs: 99 % / Redundancy: 9.3 % / Rmerge(I) obs: 0.047 / Net I/σ(I): 26.3 |
Reflection shell | Resolution: 1.45→1.54 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.274 / Mean I/σ(I) obs: 5.9 / % possible all: 94 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3VXK Resolution: 1.45→49.511 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 18.22
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.45→49.511 Å
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Refine LS restraints |
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LS refinement shell |
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