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- PDB-3tpe: The phipa p3121 structure -

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Basic information

Entry
Database: PDB / ID: 3tpe
TitleThe phipa p3121 structure
ComponentsSerine/threonine-protein kinase HipA
KeywordsTRANSFERASE / hipa / persistence / multidrug tolerance
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
HipA, N-terminal subdomain 1 / HipA N-terminal domain / HipA-like, C-terminal / HipA-like C-terminal domain
Similarity search - Domain/homology
Serine/threonine-protein kinase toxin HipA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSchumacher, M.A. / Link, T. / Brennan, R.G.
CitationJournal: 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
DepositionSep 7, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2012Group: Database references
Revision 1.2Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine/threonine-protein kinase HipA


Theoretical massNumber of molelcules
Total (without water)49,4461
Polymers49,4461
Non-polymers00
Water7,044391
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.600, 68.600, 170.500
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Serine/threonine-protein kinase HipA / Ser/Thr-protein kinase HipA / Toxin HipA


Mass: 49445.723 Da / Num. of mol.: 1
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
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 391 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.48 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.5
Details: peg 6000, pH 7.5, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 12, 2009
RadiationMonochromator: si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→85.1 Å / Num. all: 36810 / Num. obs: 36801 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 21.5 Å2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
CNS1.2refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→56.1 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2132599.06 / 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
RfactorNum. reflection% reflectionSelection details
Rfree0.243 3678 10 %RANDOM
Rwork0.184 ---
obs0.184 36743 97.7 %-
all-36810 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.7079 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 35.2 Å2
Baniso -1Baniso -2Baniso -3
1-3.9 Å20 Å20 Å2
2--3.9 Å20 Å2
3----7.8 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 1.9→56.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3347 0 0 391 3738
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.015
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d23.6
X-RAY DIFFRACTIONc_improper_angle_d1.05
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.302 592 10.8 %
Rwork0.241 4902 -
obs--89.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION5protein_rep-NEWSEP.param.txtprotein-NEWSEP.top

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