+Open data
-Basic information
Entry | Database: PDB / ID: 8hoa | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | ScRIPK mutant K124R | |||||||||
Components | Hypothetical protein | |||||||||
Keywords | PLANT PROTEIN / Kinase / RLCK VII / ScRIPK | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Saccharum hybrid cultivar (sugarcane) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.676 Å | |||||||||
Authors | Fang, J.L. / Zhang, M.Q. / Ming, Z.H. | |||||||||
Funding support | 2items
| |||||||||
Citation | Journal: Front Plant Sci / Year: 2023 Title: Receptor-like cytoplasmic kinase ScRIPK in sugarcane regulates disease resistance and drought tolerance in Arabidopsis. Authors: Fang, J. / Chai, Z. / Huang, R. / Huang, C. / Ming, Z. / Chen, B. / Yao, W. / Zhang, M. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8hoa.cif.gz | 77.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8hoa.ent.gz | 53.7 KB | Display | PDB format |
PDBx/mmJSON format | 8hoa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8hoa_validation.pdf.gz | 2.1 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8hoa_full_validation.pdf.gz | 2.1 MB | Display | |
Data in XML | 8hoa_validation.xml.gz | 14.5 KB | Display | |
Data in CIF | 8hoa_validation.cif.gz | 21.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ho/8hoa ftp://data.pdbj.org/pub/pdb/validation_reports/ho/8hoa | HTTPS FTP |
-Related structure data
Related structure data | 8ho6C 8hodC 5tosS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 36204.305 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharum hybrid cultivar (sugarcane) / Gene: NCGR_LOCUS634 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: A0A811MC32 | ||||
---|---|---|---|---|---|
#2: Chemical | ChemComp-ATP / | ||||
#3: Chemical | ChemComp-HX2 / ( | ||||
#4: Chemical | ChemComp-FMT / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.5 % |
---|---|
Crystal grow | Temperature: 289 K / Method: evaporation, recrystallization Details: 0.1 M HEPES pH 7.5, 4.3 M Sodium chloride, 40% v/v 2,5-Hexanediol, 40% v/v 2,2,2-Trifluoroethanol, 1.0 M Sodium citrate tribasic dihydrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Jan 14, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.676→82.35 Å / Num. obs: 39500 / % possible obs: 97.4 % / Redundancy: 12.937 % / CC1/2: 0.997 / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.031 / Rrim(I) all: 0.112 / Χ2: 0.97 / Net I/σ(I): 14.8 |
Reflection shell | Resolution: 1.676→1.72 Å / Num. unique obs: 2806 / CC1/2: 0.897 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5TOS Resolution: 1.676→26.441 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 21.17 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.676→26.441 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|