[English] 日本語
Yorodumi- PDB-4jhg: Crystal Structure of Medicago truncatula Nodulin 13 (MtN13) in co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4jhg | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal Structure of Medicago truncatula Nodulin 13 (MtN13) in complex with trans-zeatin | |||||||||
Components | MtN13 protein | |||||||||
Keywords | PLANT PROTEIN / PR-10 FOLD / nodulin / nodulation / legume-bacteria symbiosis / nitrogen fixation / CYTOKININ BINDING | |||||||||
Function / homology | Function and homology information nodulation / cytokinin-activated signaling pathway / response to biotic stimulus / abscisic acid binding / abscisic acid-activated signaling pathway / protein phosphatase inhibitor activity / defense response / signaling receptor activity / nucleus / cytoplasm Similarity search - Function | |||||||||
Biological species | Medicago truncatula (barrel medic) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | |||||||||
Authors | Ruszkowski, M. / Tusnio, K. / Ciesielska, A. / Brzezinski, K. / Dauter, M. / Dauter, Z. / Sikorski, M. / Jaskolski, M. | |||||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2013 Title: The landscape of cytokinin binding by a plant nodulin. Authors: Ruszkowski, M. / Szpotkowski, K. / Sikorski, M. / Jaskolski, M. #1: Journal: Febs J. / Year: 2013 Title: Structural and functional aspects of PR-10 proteins. Authors: Fernandes, H. / Michalska, K. / Sikorski, M. / Jaskolski, M. #2: Journal: J.Mol.Biol. / Year: 2008 Title: Lupinus luteus pathogenesis-related protein as a reservoir for cytokinin. Authors: Fernandes, H. / Pasternak, O. / Bujacz, G. / Bujacz, A. / Sikorski, M.M. / Jaskolski, M. #3: Journal: Febs J. / Year: 2009 Title: Cytokinin-induced structural adaptability of a Lupinus luteus PR-10 protein. Authors: Fernandes, H. / Bujacz, A. / Bujacz, G. / Jelen, F. / Jasinski, M. / Kachlicki, P. / Otlewski, J. / Sikorski, M.M. / Jaskolski, M. #4: Journal: Plant Cell / Year: 2006 Title: Crystal structure of Vigna radiata cytokinin-specific binding protein in complex with zeatin. Authors: Pasternak, O. / Bujacz, G.D. / Fujimoto, Y. / Hashimoto, Y. / Jelen, F. / Otlewski, J. / Sikorski, M.M. / Jaskolski, M. #5: Journal: Mol.Plant Microbe Interact. / Year: 1998 Title: Symbiosis-specific expression of two Medicago truncatula nodulin genes, MtN1 and MtN13, encoding products homologous to plant defense proteins. Authors: Gamas, P. / de Billy, F. / Truchet, G. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4jhg.cif.gz | 87.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4jhg.ent.gz | 64.4 KB | Display | PDB format |
PDBx/mmJSON format | 4jhg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4jhg_validation.pdf.gz | 453.9 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4jhg_full_validation.pdf.gz | 455.6 KB | Display | |
Data in XML | 4jhg_validation.xml.gz | 10.5 KB | Display | |
Data in CIF | 4jhg_validation.cif.gz | 14.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jh/4jhg ftp://data.pdbj.org/pub/pdb/validation_reports/jh/4jhg | HTTPS FTP |
-Related structure data
Related structure data | 4gy9C 4jhhC 4jhiC 2qimS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 18773.020 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Medicago truncatula (barrel medic) / Gene: MtN13 / Plasmid: PET TOPO 151D / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Magic / References: UniProt: P93330 | ||
---|---|---|---|
#2: Chemical | ChemComp-ZEA / ( | ||
#3: Chemical | ChemComp-MLI / | ||
#4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 4.02 Å3/Da / Density % sol: 69.41 % |
---|---|
Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 1.9 M SODIUM MALONATE, 200 mM NaCl, 50 mM Tris-HCl, protein was incubated overnight with trans-zeatin prior to crystallization, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 12, 2011 / Details: FOCUSING MIRRORS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: SAGITALLY FOCUSED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.85→30 Å / Num. all: 26897 / Num. obs: 26831 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 10.5 % / Rmerge(I) obs: 0.075 / Χ2: 1.092 / Net I/σ(I): 9.6 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2qim Resolution: 1.85→24.92 Å / Occupancy max: 1 / Occupancy min: 0.33 / SU ML: 0.16 / Cross valid method: R-free / Phase error: 21.92 / Stereochemistry target values: Engh & Huber / Details: Hydrogen atoms were added at riding positions
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 122.28 Å2 / Biso mean: 47.6 Å2 / Biso min: 20.67 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→24.92 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|