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- PDB-3jz3: Structure of the cytoplasmic segment of histidine kinase QseC -

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Basic information

Entry
Database: PDB / ID: 3jz3
TitleStructure of the cytoplasmic segment of histidine kinase QseC
ComponentsSensor protein qseC
KeywordsTRANSFERASE / helix-turn-helix / kinase domain / ATP-binding / Cell inner membrane / Cell membrane / Kinase / Membrane / Nucleotide-binding / Phosphoprotein / Transmembrane / Two-component regulatory system / Structural Genomics / PSI-2 / Protein Structure Initiative / Center for Structures of Membrane Proteins / CSMP
Function / homology
Function and homology information


regulation of cell motility / histidine kinase / phosphorelay signal transduction system / phosphorelay sensor kinase activity / small molecule binding / ATP binding / plasma membrane
Similarity search - Function
Two-component sensor kinase, N-terminal / Two-component sensor kinase N-terminal / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Signal transduction histidine kinase-related protein, C-terminal / Histidine kinase domain / Histidine kinase domain profile. / Histidine kinase-like ATPase, C-terminal domain ...Two-component sensor kinase, N-terminal / Two-component sensor kinase N-terminal / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Signal transduction histidine kinase-related protein, C-terminal / Histidine kinase domain / Histidine kinase domain profile. / Histidine kinase-like ATPase, C-terminal domain / Heat Shock Protein 90 / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsXie, W. / Kwiatkowski, W. / Choe, S. / Center for Structures of Membrane Proteins (CSMP)
CitationJournal: Protein Pept.Lett. / Year: 2010
Title: Structure of the Cytoplasmic Segment of Histidine Kinase Receptor QseC, a Key Player in Bacterial Virulence.
Authors: Xie, W. / Dickson, C. / Kwiatkowski, W. / Choe, S.
History
DepositionSep 22, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 21, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 4, 2012Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sensor protein qseC
B: Sensor protein qseC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5613
Polymers49,4652
Non-polymers961
Water79344
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3410 Å2
ΔGint-31 kcal/mol
Surface area14540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.737, 70.737, 176.573
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Sensor protein qseC


Mass: 24732.576 Da / Num. of mol.: 2 / Fragment: UNP residues 236-449
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: qseC, ygiY, b3026, JW2994 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P40719, histidine kinase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 2.23 Å3/Da / Density % sol: 44.91 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 8-10 mg/ml protein with 27-30% (NH4)2SO4, 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1771
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONALS 8.2.110.96789
SYNCHROTRONALS 8.2.120.9794
Detector
TypeIDDetectorDate
ADSC QUANTUM 315r1CCDAug 28, 2008
ADSC QUANTUM 315r2CCDAug 28, 2008
RadiationMonochromator: Double crystal, Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.967891
20.97941
ReflectionResolution: 2.5→50 Å / Num. all: 16338 / Num. obs: 16317 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 13.8 % / Rmerge(I) obs: 0.294 / Mean I/σ(I) obs: 10.4 / Num. unique all: 1565 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.5→34.69 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.907 / SU B: 8.426 / SU ML: 0.19 / Cross valid method: THROUGHOUT / ESU R: 0.411 / ESU R Free: 0.273 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26234 764 5.1 %RANDOM
Rwork0.22826 ---
obs0.22996 14136 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.119 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.5→34.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2308 0 5 44 2357
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0212335
X-RAY DIFFRACTIONr_angle_refined_deg0.9091.9743176
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6435304
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.78125.049103
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.36515377
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0881516
X-RAY DIFFRACTIONr_chiral_restr0.0560.2393
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.021736
X-RAY DIFFRACTIONr_nbd_refined0.1870.2913
X-RAY DIFFRACTIONr_nbtor_refined0.2950.21578
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1260.299
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1490.248
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1120.26
X-RAY DIFFRACTIONr_mcbond_it2.33521569
X-RAY DIFFRACTIONr_mcangle_it3.85332435
X-RAY DIFFRACTIONr_scbond_it2.8032836
X-RAY DIFFRACTIONr_scangle_it4.3763741
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 49 -
Rwork0.253 880 -
obs-929 100 %

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