+Open data
-Basic information
Entry | Database: PDB / ID: 6azc | ||||||
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Title | Crystal structure of Physcomitrella patens KAI2-like E S166A | ||||||
Components | Pp-KAI2-like E | ||||||
Keywords | 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 / AB hydrolase-1 domain-containing protein Function and homology information | ||||||
Biological species | Physcomitrella patens subsp. patens (plant) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.00001213332 Å | ||||||
Authors | Burger, M. / Lee, H.J. / Chory, J. | ||||||
Citation | Journal: Cell Rep / Year: 2019 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6azc.cif.gz | 141.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6azc.ent.gz | 88.5 KB | Display | PDB format |
PDBx/mmJSON format | 6azc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6azc_validation.pdf.gz | 434.6 KB | Display | wwPDB validaton report |
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Full document | 6azc_full_validation.pdf.gz | 443.2 KB | Display | |
Data in XML | 6azc_validation.xml.gz | 22.3 KB | Display | |
Data in CIF | 6azc_validation.cif.gz | 30.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/az/6azc ftp://data.pdbj.org/pub/pdb/validation_reports/az/6azc | HTTPS FTP |
-Related structure data
Related structure data | 6atxC 6azbSC 6azdC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: 1 / End auth comp-ID: ALA / End label comp-ID: ALA
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-Components
#1: Protein | Mass: 29879.115 Da / Num. of mol.: 2 / Mutation: S166A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Physcomitrella patens subsp. patens (plant) Gene: PHYPADRAFT_215526 / Plasmid: pGEX4T3 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A9ST85, Hydrolases #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 43.97 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1 M Tris, pH 8.5, 30% PEG8000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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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: Aug 17, 2017 / 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: 2→46.9 Å / Num. obs: 35204 / % possible obs: 98.73 % / Redundancy: 3.7 % / CC1/2: 0.992 / Rmerge(I) obs: 0.07743 / Rpim(I) all: 0.04693 / Net I/σ(I): 11.52 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.132 / Mean I/σ(I) obs: 8.12 / Num. unique obs: 3382 / CC1/2: 0.966 / Rpim(I) all: 0.07907 / % possible all: 97.66 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 6AZB Resolution: 2.00001213332→46.8922764945 Å / Cross valid method: FREE R-VALUE / σ(F): 5.13869702 / Phase error: 36.7910091517
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.358351877 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.00001213332→46.8922764945 Å
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Refine LS restraints |
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LS refinement shell |
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