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Open data
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Basic information
Entry | Database: PDB / ID: 5z7z | |||||||||||||||
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Title | Crystal structure of Striga hermonthica Dwarf14 (ShD14) | |||||||||||||||
![]() | Dwarf 14 | |||||||||||||||
![]() | HYDROLASE / Hydrolase Activity / putative receptor of strigolactone | |||||||||||||||
Function / homology | ![]() Alpha/beta hydrolase family / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta Similarity search - Domain/homology | |||||||||||||||
Biological species | ![]() | |||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||
![]() | Xu, Y. / Miyakawa, T. / Nakamura, A. / Tanokura, M. | |||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural analysis of HTL and D14 proteins reveals the basis for ligand selectivity in Striga. Authors: Xu, Y. / Miyakawa, T. / Nosaki, S. / Nakamura, A. / Lyu, Y. / Nakamura, H. / Ohto, U. / Ishida, H. / Shimizu, T. / Asami, T. / Tanokura, M. | |||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 126.3 KB | Display | ![]() |
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PDB format | ![]() | 96.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 468.9 KB | Display | ![]() |
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Full document | ![]() | 477.1 KB | Display | |
Data in XML | ![]() | 26.7 KB | Display | |
Data in CIF | ![]() | 38.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5z7wC ![]() 5z7xC ![]() 5z7yC ![]() 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 29819.076 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-PEG / #3: Chemical | #4: Chemical | ChemComp-EDO / #5: Water | ChemComp-HOH / | Sequence details | RESIDUE 202 IS LEU ACCORDING TO THE SEQUENCE OF GENBANK ALB07155.1. | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.7 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 10 Details: 100mM CAPS (pH 10.0), 200mM NaCl, 20% (w/v) PEG 8000 |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 31, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.978→50 Å / Num. obs: 36505 / % possible obs: 99.6 % / Redundancy: 3.8 % / CC1/2: 0.999 / Rrim(I) all: 0.065 / Net I/σ(I): 17.6 |
Reflection shell | Resolution: 1.978→2.03 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 3 / Num. unique obs: 2707 / CC1/2: 0.872 / Rrim(I) all: 0.582 / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3VXK Resolution: 1.978→38.313 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.72
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.978→38.313 Å
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Refine LS restraints |
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LS refinement shell |
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