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Yorodumi- PDB-6cth: Crystal Structure of Pathogenesis-related Protein 1G (PR-1G) Kina... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6cth | ||||||
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Title | Crystal Structure of Pathogenesis-related Protein 1G (PR-1G) Kinase Domain from Cacao | ||||||
Components | Concanavalin A-like lectin protein kinase family protein | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / Structural Genomics / Structural Genomics Consortium / SGC / Transferase-Transferase Inhibitor complex | ||||||
Function / homology | Function and homology information defense response to oomycetes / transmembrane receptor protein serine/threonine kinase activity / defense response / carbohydrate binding / membrane => GO:0016020 / defense response to bacterium / extracellular region / ATP binding / plasma membrane Similarity search - Function | ||||||
Biological species | Theobroma cacao (cacao) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Tosarini, T.R. / Profeta, G.S. / dos Reis, C.V. / Counago, R.M. / Massirer, K.B. / Edwards, A.M. / Elkins, J.M. / Structural Genomics Consortium (SGC) | ||||||
Funding support | Brazil, 1items
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Citation | Journal: To Be Published Title: Crystal Structure of Pathogenesis-related Protein 1G (PR-1G) Kinase Domain from Cacao Authors: Tosarini, T.R. / Profeta, G.S. / dos Reis, C.V. / Counago, R.M. / Massirer, K.B. / Mondego, J.M.C. / Edwards, A.M. / Elkins, J.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6cth.cif.gz | 135.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6cth.ent.gz | 102.6 KB | Display | PDB format |
PDBx/mmJSON format | 6cth.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ct/6cth ftp://data.pdbj.org/pub/pdb/validation_reports/ct/6cth | HTTPS FTP |
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-Related structure data
Related structure data | 3uimS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 34698.035 Da / Num. of mol.: 1 / Fragment: kinase domain (UNP residues 255-560) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Theobroma cacao (cacao) / Gene: TCM_042446 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): R3 / References: UniProt: A0A061FLD4 |
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#2: Chemical | ChemComp-FE7 / |
#3: Chemical | ChemComp-MG / |
#4: Chemical | ChemComp-ACT / |
#5: 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: 2.4 Å3/Da / Density % sol: 48.8 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 18% PEG8000, 0.2 M magnesium acetate, 0.1 M SSB buffer |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 12, 2017 |
Radiation | Monochromator: Cryo-cooled double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→30 Å / Num. obs: 39498 / % possible obs: 100 % / Redundancy: 18.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.02 / Rrim(I) all: 0.086 / Net I/σ(I): 17.4 |
Reflection shell | Resolution: 1.7→1.73 Å / Redundancy: 18.8 % / Rmerge(I) obs: 1.73 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 2030 / CC1/2: 0.829 / Rpim(I) all: 0.544 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3UIM Resolution: 1.7→30 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.95 / SU B: 5.977 / SU ML: 0.098 / Cross valid method: THROUGHOUT / ESU R: 0.108 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.402 Å2
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Refinement step | Cycle: 1 / Resolution: 1.7→30 Å
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Refine LS restraints |
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