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Yorodumi- PDB-4g78: Subatomic Resolution Crystal Structure of Histidine-containing Ph... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4g78 | ||||||
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Title | Subatomic Resolution Crystal Structure of Histidine-containing Phosphotransfer Protein MtHPt2 from Medicago truncatula | ||||||
Components | Histidine phosphotransfer protein | ||||||
Keywords | TRANSFERASE / SUBATOMIC RESOLUTION / HELIX BUNDLE / PLANT HORMONE SIGNAL TRANSDUCTION / HISTIDINE KINASE | ||||||
Function / homology | Function and homology information protein histidine kinase binding / cytokinin-activated signaling pathway / histidine phosphotransfer kinase activity / phosphorelay signal transduction system / phosphorylation / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Medicago truncatula (barrel medic) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 0.92 Å | ||||||
Authors | Ruszkowski, M. / Sikorski, M. / Jaskolski, M. | ||||||
Citation | Journal: To be Published Title: Subatomic Resolution Crystal Structure of Histidine-containing Phosphotransfer Protein MtHPt2 from Medicago truncatula Authors: Ruszkowski, M. / 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: Journal: Protein Sci. / Year: 2005 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: Journal: J.Mol.Biol. / Year: 1999 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4g78.cif.gz | 88.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4g78.ent.gz | 67.5 KB | Display | PDB format |
PDBx/mmJSON format | 4g78.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g7/4g78 ftp://data.pdbj.org/pub/pdb/validation_reports/g7/4g78 | HTTPS FTP |
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-Related structure data
Related structure data | 3us6S 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: 17475.738 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Medicago truncatula (barrel medic) / Gene: MtHPt2, MTR_1g089130, MTR_1g089350 / Plasmid: pMCSG48 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Magic References: UniProt: G7I2T8, 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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.81 Å3/Da / Density % sol: 32.01 % |
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Crystal grow | Temperature: 292 K / pH: 6.5 Details: 0.09M Halogens, 0.1M buffer system 1, 30% PEG 550MME + PEG 20K (Molecular Dimensions Morpheus Screen B1), pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 17, 2012 / Details: FOCUSING MIRRORS |
Radiation | Monochromator: SAGITALLY FOCUSED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 0.92→50 Å / Num. obs: 84634 / % possible obs: 97.8 % / Observed criterion σ(I): -3 / Redundancy: 6.3 % / Biso Wilson estimate: 13.232 Å2 / Rmerge(I) obs: 0.036 / Net I/σ(I): 21.78 |
Reflection shell | Resolution: 0.92→0.94 Å / Rmerge(I) obs: 0.738 / Mean I/σ(I) obs: 1.89 / % possible all: 75.1 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3US6 Resolution: 0.92→50 Å / Cross valid method: R-FREE / Stereochemistry target values: Engh & Huber / Details: HYDROGEN ATOMS WERE ADDED AT RIDING POSITIONS
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Solvent computation | Solvent model: BABINET MODEL | |||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.627 Å2 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.92→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 0.92→0.96 Å / Rfactor Rwork: 0.271 |