+Open data
-Basic information
Entry | Database: PDB / ID: 3tpb | ||||||
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Title | Structure of HipA(S150A) | ||||||
Components | Serine/threonine-protein kinase HipA | ||||||
Keywords | TRANSFERASE / hipA / persistenct / multidrug tolerance / HipB / authophosphorylation / P-loop | ||||||
Function / homology | Function and homology information dormancy process / toxin-antitoxin complex / single-species biofilm formation / regulation of growth / DNA-binding transcription repressor activity / protein-DNA complex / sequence-specific DNA binding / non-specific serine/threonine protein kinase / transcription cis-regulatory region binding / phosphorylation ...dormancy process / toxin-antitoxin complex / single-species biofilm formation / regulation of growth / DNA-binding transcription repressor activity / protein-DNA complex / sequence-specific DNA binding / non-specific serine/threonine protein kinase / transcription cis-regulatory region binding / phosphorylation / response to antibiotic / protein serine kinase activity / protein serine/threonine kinase activity / regulation of DNA-templated transcription / magnesium ion binding / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å | ||||||
Authors | schumacher, M.A. | ||||||
Citation | Journal: Cell Rep / Year: 2012 Title: Role of Unusual P Loop Ejection and Autophosphorylation in HipA-Mediated Persistence and Multidrug Tolerance. Authors: Schumacher, M.A. / Min, J. / Link, T.M. / Guan, Z. / Xu, W. / Ahn, Y.H. / Soderblom, E.J. / Kurie, J.M. / Evdokimov, A. / Moseley, M.A. / Lewis, K. / Brennan, R.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3tpb.cif.gz | 97.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3tpb.ent.gz | 73.4 KB | Display | PDB format |
PDBx/mmJSON format | 3tpb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3tpb_validation.pdf.gz | 440.8 KB | Display | wwPDB validaton report |
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Full document | 3tpb_full_validation.pdf.gz | 447.5 KB | Display | |
Data in XML | 3tpb_validation.xml.gz | 19.1 KB | Display | |
Data in CIF | 3tpb_validation.cif.gz | 27.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tp/3tpb ftp://data.pdbj.org/pub/pdb/validation_reports/tp/3tpb | HTTPS FTP |
-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: 49362.789 Da / Num. of mol.: 1 / Mutation: S150A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: hipA / Production host: Escherichia coli (E. coli) References: UniProt: P23874, non-specific serine/threonine protein kinase | ||
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#2: Chemical | ChemComp-CL / | ||
#3: Chemical | #4: 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: 2.07 Å3/Da / Density % sol: 40.63 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 14% PEG 8000, 20% glycerol and 0.04 M potassium phosphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.02 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 12, 2009 |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.02 Å / Relative weight: 1 |
Reflection | Resolution: 1.88→84.5 Å / Num. obs: 29360 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 22 Å2 |
Reflection shell | Resolution: 1.88→1.92 Å / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.88→50 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1086865.92 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 60.8458 Å2 / ksol: 0.4 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.88→50 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: NONE | |||||||||||||||||||||||||
Xplor file |
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