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- PDB-3us6: Crystal Structure of Histidine-containing Phosphotransfer Protein... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3us6 | ||||||
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Title | Crystal Structure of Histidine-containing Phosphotransfer Protein MtHPt1 from Medicago truncatula | ||||||
![]() | Histidine-containing Phosphotransfer Protein type 1, MtHPt1 | ||||||
![]() | TRANSFERASE / helix bundle / PLANT HORMONE SIGNAL TRANSDUCTION / CYTOKININ SIGNAL TRANSDUCTION / PHOSPHORYLATION / PHOSPHATE TRANSFER RELAY / RESPONSE REGULATOR / SIGNALING PROTEIN / CYTOKININ RECEPTOR CRE1 | ||||||
Function / homology | ![]() multidimensional cell growth / embryo sac development / protein histidine kinase binding / cytokinin-activated signaling pathway / histidine phosphotransfer kinase activity / phosphorelay signal transduction system / phosphorylation / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Ruszkowski, M. / Brzezinski, K. / Jedrzejczak, R. / Dauter, M. / Dauter, Z. / Sikorski, M. / Jaskolski, M. | ||||||
![]() | ![]() Title: Medicago truncatula histidine-containing phosphotransfer protein: Structural and biochemical insights into the cytokinin transduction pathway in plants. Authors: Ruszkowski, M. / Brzezinski, K. / Jedrzejczak, R. / Dauter, M. / Dauter, Z. / Sikorski, M. / Jaskolski, M. #1: Journal: Plant Cell / Year: 2006 Title: The Arabidopsis histidine phosphotransfer proteins are redundant positive regulators of cytokinin signaling. Authors: Hutchison, C.E. / Li, J. / Argueso, C. / Gonzalez, M. / Lee, E. / Lewis, M.W. / Maxwell, B.B. / Perdue, T.D. / Schaller, G.E. / Alonso, J.M. / Ecker, J.R. / Kieber, J.J. #2: ![]() Title: Crystal structure of the histidine-containing phosphotransfer protein ZmHP2 from maize. Authors: Sugawara, H. / Kawano, Y. / Hatakeyama, T. / Yamaya, T. / Kamiya, N. / Sakakibara, H. #3: ![]() Title: Conservation of structure and function among histidine-containing phosphotransfer (HPt) domains as revealed by the crystal structure of YPD1. Authors: Xu, Q. / West, A.H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 79.5 KB | Display | ![]() |
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PDB format | ![]() | 59.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 413.9 KB | Display | ![]() |
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Full document | ![]() | 416.3 KB | Display | |
Data in XML | ![]() | 9.4 KB | Display | |
Data in CIF | ![]() | 13.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1yviS S: Starting model for refinement |
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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: 17782.297 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: B7FGU6, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with a nitrogenous group as acceptor |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 41.17 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.1M BIS-TRIS, 25% PEG 3350, 0.2M AMMONIUM ACETATE, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 25, 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: 1.446→50 Å / Num. all: 25816 / Num. obs: 25816 / % possible obs: 94.3 % / Observed criterion σ(I): -3 / Redundancy: 3.81 % / Biso Wilson estimate: 22.723 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 14.05 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1yvi Resolution: 1.446→31.037 Å / Occupancy max: 1 / Occupancy min: 0.29 / SU ML: 0.33 / Cross valid method: Rfree / Phase error: 17.8 / Stereochemistry target values: Engh & Huber / Details: HYDROGEN ATOMS WERE ADDED AT RIDING POSITIONS
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Solvent computation | Shrinkage radii: 0.53 Å / VDW probe radii: 0.7 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.291 Å2 / ksol: 0.405 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 151.57 Å2 / Biso mean: 23.0623 Å2 / Biso min: 7.97 Å2
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Refinement step | Cycle: LAST / Resolution: 1.446→31.037 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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