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Yorodumi- PDB-3dgf: Structure of a histidine kinase-response regulator complex reveal... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3dgf | ||||||
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Title | Structure of a histidine kinase-response regulator complex reveals insights into Two-component signaling and a novel cis-autophosphorylation mechanism | ||||||
Components | Response regulator | ||||||
Keywords | SIGNALING PROTEIN / receiver domain | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Thermotoga maritima (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å | ||||||
Authors | Casino, P. / Marina, A. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2009 Title: Structural Insight into Partner Specificity and Phosphoryl Transfer in Two-Component Signal Transduction. Authors: Casino, P. / Rubio, V. / Marina, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3dgf.cif.gz | 39.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3dgf.ent.gz | 27.8 KB | Display | PDB format |
PDBx/mmJSON format | 3dgf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dg/3dgf ftp://data.pdbj.org/pub/pdb/validation_reports/dg/3dgf | HTTPS FTP |
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-Related 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: 13848.256 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM_0468 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): RIL / References: UniProt: Q9WYT9 |
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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: 2.02 Å3/Da / Density % sol: 39.2 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 28% PEG8000, 0.2M ammonium sulfate, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM16 / Wavelength: 1.008 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jan 1, 2005 / Details: mirror |
Radiation | Monochromator: Si(111), 140 x 80 x 20 mm / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.008 Å / Relative weight: 1 |
Reflection | Resolution: 2→22.1 Å / Num. all: 7951 / Num. obs: 40193 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 5.1 % / Biso Wilson estimate: 32.7 Å2 / Rmerge(I) obs: 0.088 / Rsym value: 0.088 / Net I/σ(I): 8.8 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.383 / Mean I/σ(I) obs: 3.9 / Num. unique all: 1143 / Rsym value: 0.383 / % possible all: 100 |
-Processing
Software |
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Refinement | Starting model: RR468 from the entry 2008-Jun-12.09.34.07.979392.Session.11388 Resolution: 2→22.1 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.904 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 10.129 / SU ML: 0.144 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.258 / ESU R Free: 0.205 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 73.93 Å2 / Biso mean: 34.57 Å2 / Biso min: 15.79 Å2
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Refinement step | Cycle: LAST / Resolution: 2→22.1 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
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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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