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- PDB-3kyz: The crystal structure of the sensor domain of two-component senso... -

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Basic information

Entry
Database: PDB / ID: 3kyz
TitleThe crystal structure of the sensor domain of two-component sensor PfeS from Pseudomonas aeruginosa PA01
ComponentsSensor protein pfeS
KeywordsTRANSFERASE / APC37897.4 / the sensor domain of two-component sensor PfeS / Pseudomonas aeruginosa PA01 / structural genomics / PSI-2 / protein structure initiative / midwest center for structural genomics / MCSG / ATP-binding / Cell inner membrane / Cell membrane / Kinase / Membrane / Nucleotide-binding / Phosphoprotein / Transmembrane / Two-component regulatory system
Function / homology
Function and homology information


histidine kinase / phosphorelay sensor kinase activity / phosphorelay signal transduction system / membrane => GO:0016020 / ATP binding / plasma membrane
Similarity search - Function
Two-component histidine kinase, sensor domain / Two-component histidine kinase, sensor domain / Two-component histidine kinase, sensor domain superfamily / Sensor domain of 2-component histidine kinase / HAMP domain / HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain / HAMP domain profile. / HAMP domain / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain ...Two-component histidine kinase, sensor domain / Two-component histidine kinase, sensor domain / Two-component histidine kinase, sensor domain superfamily / Sensor domain of 2-component histidine kinase / HAMP domain / HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain / HAMP domain profile. / HAMP domain / 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. / Beta-Lactamase / 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
FORMIC ACID / Sensor protein PfeS
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.497 Å
AuthorsTan, K. / Marshall, N. / Buck, K. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of the sensor domain of two-component sensor PfeS from Pseudomonas aeruginosa PA01
Authors: Tan, K. / Marshall, N. / Buck, K. / Joachimiak, A.
History
DepositionDec 7, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sensor protein pfeS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4845
Polymers14,3321
Non-polymers1524
Water2,684149
1
A: Sensor protein pfeS
hetero molecules

A: Sensor protein pfeS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,96810
Polymers28,6632
Non-polymers3058
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-y+1/2,z1
Buried area2960 Å2
ΔGint-77 kcal/mol
Surface area11050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)29.920, 95.468, 103.565
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121

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Components

#1: Protein Sensor protein pfeS /


Mass: 14331.721 Da / Num. of mol.: 1 / Fragment: sequence database residues 28-149
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PA01 / Gene: pfeS, PA2687 / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): pPK1037 / References: UniProt: Q04804, histidine kinase
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 149 / 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: 2.58 Å3/Da / Density % sol: 52.33 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2M MgCl2, 0.1M Bis-Tris, 25% PEG3350, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97932 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 11, 2009 / Details: mirror
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97932 Å / Relative weight: 1
ReflectionResolution: 1.5→35 Å / Num. all: 24347 / Num. obs: 24347 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.5 % / Biso Wilson estimate: 16.1 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 41.4
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.731 / Mean I/σ(I) obs: 2.5 / Num. unique all: 1145 / % possible all: 97.4

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXDphasing
MLPHAREphasing
DMmodel building
ARPmodel building
WARPmodel building
HKL-3000phasing
PHENIX(phenix.refine: 1.5_2)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RefinementMethod to determine structure: SAD / Resolution: 1.497→35 Å / SU ML: 0.15 / σ(F): 0.04 / Phase error: 14.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1811 1198 5.09 %random
Rwork0.1511 ---
obs0.1527 23518 96.13 %-
all-23518 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.341 Å2 / ksol: 0.347 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.8912 Å2-0 Å20 Å2
2---0.9166 Å2-0 Å2
3---3.8078 Å2
Refinement stepCycle: LAST / Resolution: 1.497→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms963 0 6 149 1118
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005999
X-RAY DIFFRACTIONf_angle_d0.9571361
X-RAY DIFFRACTIONf_dihedral_angle_d17.028392
X-RAY DIFFRACTIONf_chiral_restr0.064137
X-RAY DIFFRACTIONf_plane_restr0.004182
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4971-1.55710.21291130.16932152X-RAY DIFFRACTION85
1.5571-1.62790.17541140.13282305X-RAY DIFFRACTION91
1.6279-1.71370.14461360.11092408X-RAY DIFFRACTION95
1.7137-1.82110.16881450.10512437X-RAY DIFFRACTION97
1.8211-1.96170.15541420.10682537X-RAY DIFFRACTION99
1.9617-2.15910.15321320.11352551X-RAY DIFFRACTION99
2.1591-2.47150.1871420.13342579X-RAY DIFFRACTION100
2.4715-3.11350.1691300.15712622X-RAY DIFFRACTION100
3.1135-35.10680.18811440.16972729X-RAY DIFFRACTION99

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