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Yorodumi- PDB-2qvg: The crystal structure of a two-component response regulator from ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2qvg | ||||||
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Title | The crystal structure of a two-component response regulator from Legionella pneumophila | ||||||
Components | Two component response regulator | ||||||
Keywords | TRANSFERASE / 11016o / NYSGXRC / two component response regulator / PSI-2 / Structural Genomics / Protein Structure Initiative / New York SGX Research Center for Structural Genomics | ||||||
Function / homology | Function and homology information Transferases; Transferring phosphorus-containing groups; Phosphotransferases with a nitrogenous group as acceptor / phosphorelay signal transduction system / transferase activity Similarity search - Function | ||||||
Biological species | Legionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å | ||||||
Authors | Tyagi, R. / Eswaramoorthy, S. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: To be Published Title: The crystal structure of a two-component response regulator from Legionella pneumophila. Authors: Tyagi, R. / Eswaramoorthy, S. / Burley, S.K. / Swaminathan, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2qvg.cif.gz | 38.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2qvg.ent.gz | 29.1 KB | Display | PDB format |
PDBx/mmJSON format | 2qvg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qv/2qvg ftp://data.pdbj.org/pub/pdb/validation_reports/qv/2qvg | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 16692.590 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Legionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria) Species: Legionella pneumophila / Strain: Philadelphia 1, DSM 7513 / Gene: lpg2457 / Plasmid: pSGX3-BC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: Q5ZSR0, 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: 2.38 Å3/Da / Density % sol: 48.34 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.2M Lithium sulfate, 0.1M Bis-Tris pH 5.5, 25% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9791 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 3, 2007 / Details: Mirrors |
Radiation | Monochromator: Si(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. all: 44110 / Num. obs: 44110 / % possible obs: 89.1 % / Redundancy: 9.5 % / Biso Wilson estimate: 16.4 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 21.7 |
Reflection shell | Resolution: 1.5→1.55 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.156 / Mean I/σ(I) obs: 7 / Num. unique all: 2265 / % possible all: 45.6 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.5→40.2 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 1225649.46 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: The Bijvoet differences were used for phasing. Residues listed as missing in Remark 465 are due to lack of electron density. Residues with missing atoms listed in Remark 470 are due to lack ...Details: The Bijvoet differences were used for phasing. Residues listed as missing in Remark 465 are due to lack of electron density. Residues with missing atoms listed in Remark 470 are due to lack of electron density for side chains and modeled as alanines.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 45.9937 Å2 / ksol: 0.399418 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.5→40.2 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.59 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
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Xplor file |
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