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Yorodumi- PDB-2q4f: Ensemble refinement of the crystal structure of putative histidin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2q4f | ||||||
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Title | Ensemble refinement of the crystal structure of putative histidine-containing phosphotransfer protein from rice, Ak104879 | ||||||
Components | Histidine-containing phosphotransfer protein 1 | ||||||
Keywords | SIGNALING PROTEIN / Ensemble Refinement / Refinement Methodology Development / AK104879 / PHOSPHORELAY MEDIATOR / HP1 / Structural Genomics / Protein Structure Initiative / PSI / Center for Eukaryotic Structural Genomics / CESG | ||||||
Function / homology | Function and homology information positive regulation of cytokinin-activated signaling pathway / 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 | Oryza sativa (Asian cultivated rice) | ||||||
Method | X-RAY DIFFRACTION / Re-refinement using ensemble model / Resolution: 2 Å | ||||||
Authors | Levin, E.J. / Kondrashov, D.A. / Wesenberg, G.E. / Phillips Jr., G.N. / Center for Eukaryotic Structural Genomics (CESG) | ||||||
Citation | Journal: Structure / Year: 2007 Title: Ensemble refinement of protein crystal structures: validation and application. Authors: Levin, E.J. / Kondrashov, D.A. / Wesenberg, G.E. / Phillips, G.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2q4f.cif.gz | 452.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2q4f.ent.gz | 395.1 KB | Display | PDB format |
PDBx/mmJSON format | 2q4f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2q4f_validation.pdf.gz | 576.6 KB | Display | wwPDB validaton report |
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Full document | 2q4f_full_validation.pdf.gz | 686.9 KB | Display | |
Data in XML | 2q4f_validation.xml.gz | 121.2 KB | Display | |
Data in CIF | 2q4f_validation.cif.gz | 166.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q4/2q4f ftp://data.pdbj.org/pub/pdb/validation_reports/q4/2q4f | HTTPS FTP |
-Related structure data
Related structure data | 2q3mC 2q3oC 2q3pC 2q3qC 2q3rC 2q3sC 2q3tC 2q3uC 2q3vC 2q3wC 2q40C 2q41C 2q42C 2q43C 2q44C 2q45C 2q46C 2q47C 2q48C 2q49C 2q4aC 2q4bC 2q4cC 2q4dC 2q4eC 2q4hC 2q4iC 2q4jC 2q4kC 2q4lC 2q4mC 2q4nC 2q4oC 2q4pC 2q4qC 2q4rC 2q4sC 2q4tC 2q4uC 2q4vC 2q4xC 2q4yC 2q4zC 2q50C 2q51C 2q52C 1yviS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Number of models | 8 |
-Components
#1: Protein | Mass: 16780.982 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryza sativa (Asian cultivated rice) / Strain: cv. Japonica Gene: HP1, AK104879, Os09g0567400, LOC_Os09g39400, OJ1155_H10.30 Plasmid: PVP-13 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) P(LACI+RARE) / References: UniProt: Q6VAK4 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 55.6 % / Description: AUTHOR USED THE SF DATA FROM ENTRY 1YVI. |
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-Data collection
Detector | Type: APS-1 |
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Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
-Processing
Software |
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Refinement | Method to determine structure: Re-refinement using ensemble model Starting model: PDB entry 1YVI Resolution: 2→37.77 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2337234.5 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Stereochemistry target values: maximum likelihood using amplitudes Details: This PDB entry is a re-refinement using an ensemble model of the previously deposited single-conformer structure 1yvi and the first data set in the deposited structure factor file for 1yvi ...Details: This PDB entry is a re-refinement using an ensemble model of the previously deposited single-conformer structure 1yvi and the first data set in the deposited structure factor file for 1yvi along with the R-free set defined therein. The coordinates were generated by an automated protocol from an initial model consisting of 8 identical copies of the protein and non-water hetero-atoms assigned fractional occupancies adding up to one, and a single copy of the solvent molecules. Refinement was carried out with all the conformers present simultaneously and with the potential energy terms corresponding to interactions between the different conformers excluded. The helix and sheet records were calculated using coordinates from the first conformer only. The structure visualization program PYMOL is well-suited for directly viewing the ensemble model presented in this PDB file.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 46.656 Å2 / ksol: 0.355 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→37.77 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: 6
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Xplor file |
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