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Open data
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Basic information
Entry | Database: PDB / ID: 6azd | ||||||
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Title | Crystal structure of Physcomitrella patens KAI2-like H | ||||||
![]() | PpKAI2-like H | ||||||
![]() | HYDROLASE / alpha/beta hydrolase / strigolactone binding | ||||||
Function / homology | alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Predicted protein![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Burger, M. / Lee, H.J. / Chory, J. | ||||||
![]() | ![]() Title: Structural Basis of Karrikin and Non-natural Strigolactone Perception in Physcomitrella patens. Authors: Burger, M. / Mashiguchi, K. / Lee, H.J. / Nakano, M. / Takemoto, K. / Seto, Y. / Yamaguchi, S. / Chory, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 81.9 KB | Display | ![]() |
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PDB format | ![]() | 48.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 419.4 KB | Display | ![]() |
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Full document | ![]() | 421.8 KB | Display | |
Data in XML | ![]() | 12.8 KB | Display | |
Data in CIF | ![]() | 18 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6atxC ![]() 6azbC ![]() 6azcC ![]() 4jypS 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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Unit cell |
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Components
#1: Protein | Mass: 29864.607 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: PHYPADRAFT_184560 / Plasmid: pGEX4T3 / Production host: ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.75 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 1.8 M ammonium sulfate, 0.1 M MES 6.5, 5% PEG400 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 8, 2016 / Details: mirrors |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.97→37.1 Å / Num. obs: 18745 / % possible obs: 98.31 % / Redundancy: 3.5 % / CC1/2: 0.982 / Rmerge(I) obs: 0.1674 / Rpim(I) all: 0.1065 / Net I/σ(I): 8.17 |
Reflection shell | Resolution: 1.97→2.04 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.4449 / Mean I/σ(I) obs: 3.85 / Num. unique obs: 1833 / CC1/2: 0.549 / Rpim(I) all: 0.285 / % possible all: 97.66 |
-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 4JYP Resolution: 1.97010740396→37.0182176364 Å / SU ML: 0.277465883878 / Cross valid method: FREE R-VALUE / σ(F): 1.3487061327 / Phase error: 24.1330848868
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.9028463926 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.97010740396→37.0182176364 Å
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Refine LS restraints |
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LS refinement shell |
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