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Yorodumi- PDB-4jau: Structural basis of a rationally rewired protein-protein interfac... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4jau | ||||||
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Title | Structural basis of a rationally rewired protein-protein interface (HK853mutant A268V, A271G, T275M, V294T and D297E) | ||||||
Components | Histidine kinase | ||||||
Keywords | TRANSFERASE / Bergerat fold / Four-helix bundle / Signal transduction / Histidine kinase / Autophosphorylation / Phosphatase / Response regulator RR468 | ||||||
Function / homology | Function and homology information histidine phosphotransfer kinase activity / histidine kinase / phosphorelay sensor kinase activity / nucleotide binding / identical protein binding / metal ion binding Similarity search - Function | ||||||
Biological species | Thermotoga maritima (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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 | 4jau.cif.gz | 111.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4jau.ent.gz | 85.6 KB | Display | PDB format |
PDBx/mmJSON format | 4jau.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4jau_validation.pdf.gz | 806.2 KB | Display | wwPDB validaton report |
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Full document | 4jau_full_validation.pdf.gz | 809.6 KB | Display | |
Data in XML | 4jau_validation.xml.gz | 11.5 KB | Display | |
Data in CIF | 4jau_validation.cif.gz | 15.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ja/4jau ftp://data.pdbj.org/pub/pdb/validation_reports/ja/4jau | HTTPS FTP |
-Related structure data
Related structure data | 4ja2C 4jasC 4javC 2c2aS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 29438.402 Da / Num. of mol.: 1 / Fragment: HK853 cytoplasmic region, UNP residues 232-489 / Mutation: A268V, A271G, T275M, V294T, D297E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: MSB8 / Gene: TM_0853 / Plasmid: pET24 / Production host: Escherichia coli (E. coli) / Strain (production host): K-12 / References: UniProt: Q9WZV7, histidine kinase |
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#2: Chemical | ChemComp-ADP / |
#3: 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: 2.45 Å3/Da / Density % sol: 49.78 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 8% PEG4000, 0.8M lithium chloride, Tris, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9173 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 10, 2011 / Details: toroidal mirrors |
Radiation | Monochromator: Single bounce monochromator 28m / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9173 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→73 Å / Num. obs: 8277 / % possible obs: 99.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.057 |
Reflection shell | Resolution: 2.7→2.85 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.337 / Mean I/σ(I) obs: 21 / Num. unique all: 8277 / Rsym value: 0.337 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2C2A Resolution: 2.7→44.78 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.903 / SU B: 35.712 / SU ML: 0.373 / Cross valid method: THROUGHOUT / σ(F): 2.3 / ESU R Free: 0.392 / 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: 70.365 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→44.78 Å
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Refine LS restraints |
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LS refinement shell | Highest resolution: 2.7 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: -18.8408 Å / Origin y: 17.9942 Å / Origin z: -4.4024 Å
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