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Yorodumi- PDB-4ja2: Structural basis of a rationally rewired protein-protein interfac... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ja2 | ||||||
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Title | Structural basis of a rationally rewired protein-protein interface (RR468mutant V13P, L14I, I17M and N21V) | ||||||
Components | Response regulator | ||||||
Keywords | SIGNALING PROTEIN / alpha/beta domain / signal propagation / catalysis of phosphotransfer / auto-dephosphorylation / Histidine kinase binding / Phosphorylation | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Thermotoga maritima (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å | ||||||
Authors | Podgornaia, A.I. / Casino, P. / Marina, A. / Laub, M.T. | ||||||
Citation | Journal: Structure / Year: 2013 Title: Structural basis of a rationally rewired protein-protein interface critical to bacterial signaling Authors: Podgornaia, A.I. / Casino, P. / Marina, A. / Laub, M.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ja2.cif.gz | 41 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ja2.ent.gz | 27.3 KB | Display | PDB format |
PDBx/mmJSON format | 4ja2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ja/4ja2 ftp://data.pdbj.org/pub/pdb/validation_reports/ja/4ja2 | HTTPS FTP |
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-Related structure data
Related structure data | 4jasC 4jauC 4javC 3gl9S C: citing same article (ref.) 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: 13914.305 Da / Num. of mol.: 1 / Mutation: V13P, L14I, I17M, N21V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: MSB8 / Gene: TM_0468 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): K-12 / References: UniProt: Q9WYT9 | ||
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#2: Chemical | ChemComp-MG / | ||
#3: Chemical | ChemComp-SO4 / | ||
#4: Chemical | #5: 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: 2.01 Å3/Da / Density % sol: 38.87 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 50% PEG400, 0.1M sodium acetate, 0.2M lithium sulfate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 29, 2011 Details: Pt coated mirrors in a Kirkpatrick-Baez (KB) geometry |
Radiation | Monochromator: Si (111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 1.79→35.74 Å / Num. obs: 10950 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.078 |
Reflection shell | Resolution: 1.79→1.88 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.279 / Mean I/σ(I) obs: 19.6 / Num. unique all: 10950 / Rsym value: 0.279 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3GL9 Resolution: 1.79→35.74 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.923 / SU B: 2.476 / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 2.6 / ESU R: 0.143 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.5 Å2
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Refinement step | Cycle: LAST / Resolution: 1.79→35.74 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.79→1.836 Å / Total num. of bins used: 20
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