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- PDB-3kkb: The crystal structure of a two-component sensor domain from Pseud... -

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Basic information

Entry
Database: PDB / ID: 3kkb
TitleThe crystal structure of a two-component sensor domain from Pseudomonas aeruginosa PA01
ComponentsSensor protein
KeywordsTRANSFERASE / APC37838.3 / two-component sensor / Pseudomonas aeruginosa PA01 / structural genomics / PSI-2 / protein structure initiative / midwest center for structural genomics / MCSG / ATP-binding / Kinase / Membrane / Nucleotide-binding / Phosphoprotein / Transmembrane
Function / homology
Function and homology information


alginic acid biosynthetic process / histidine kinase / phosphatase activity / phosphorelay sensor kinase activity / membrane => GO:0016020 / ATP binding / membrane / plasma membrane
Similarity search - Function
Histidine kinase (KinB), sensor domain / Alginate biosynthesis sensor protein KinB, sensor domain / KinB, N-terminal domain superfamily / Sensor domain of alginate biosynthesis sensor protein KinB / PAS fold-4 / PAS fold / HAMP domain / HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain / HAMP domain profile. / HAMP domain ...Histidine kinase (KinB), sensor domain / Alginate biosynthesis sensor protein KinB, sensor domain / KinB, N-terminal domain superfamily / Sensor domain of alginate biosynthesis sensor protein KinB / PAS fold-4 / PAS fold / 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. / PAS domain / Four Helix Bundle (Hemerythrin (Met), subunit A) / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / PAS domain / Histidine kinase-like ATPases / PAS domain superfamily / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
PHOSPHATE ION / Alginate biosynthesis sensor protein KinB / histidine kinase
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.881 Å
AuthorsTan, K. / Chhor, G. / Buck, K. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of a two-component sensor domain from Pseudomonas aeruginosa PA01
Authors: Tan, K. / Chhor, G. / Buck, K. / Joachimiak, A.
History
DepositionNov 5, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 17, 2009Provider: 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
B: Sensor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3054
Polymers29,1152
Non-polymers1902
Water3,261181
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5110 Å2
ΔGint-64 kcal/mol
Surface area12520 Å2
Unit cell
Length a, b, c (Å)75.361, 75.361, 75.020
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
DetailsExperimentally unknown. The chains A and B are predicted to form a dimer.

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Components

#1: Protein Sensor protein / a two-component sensor domain


Mass: 14557.721 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Strain: PA01 / Gene: PA5484, Pseudomonas aeruginosa / Plasmid: pMCSG9 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: Q9HT87, UniProt: O34206*PLUS, histidine kinase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 181 / 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: 2.11 Å3/Da / Density % sol: 41.77 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 0.1M Phosphate-citrate, 1.6M NaH2PO4 /0.4M K2HPO4, pH 4.2, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97942 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 16, 2009 / Details: Mirror
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97942 Å / Relative weight: 1
ReflectionResolution: 1.88→38 Å / Num. all: 20202 / Num. obs: 20202 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 23.8
Reflection shellResolution: 1.88→1.91 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.541 / Mean I/σ(I) obs: 2.3 / Num. unique all: 854 / % possible all: 86.3

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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: 1.881→37.68 Å / SU ML: 0.22 / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2201 982 5.03 %RANDOM
Rwork0.1634 ---
all0.1662 19520 --
obs0.1662 19520 95.62 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.992 Å2 / ksol: 0.345 e/Å3
Refinement stepCycle: LAST / Resolution: 1.881→37.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2006 0 10 181 2197
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062040
X-RAY DIFFRACTIONf_angle_d0.8762766
X-RAY DIFFRACTIONf_dihedral_angle_d18.157776
X-RAY DIFFRACTIONf_chiral_restr0.056309
X-RAY DIFFRACTIONf_plane_restr0.003383
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8813-1.98050.24721170.19062240X-RAY DIFFRACTION82
1.9805-2.10450.21461420.16252573X-RAY DIFFRACTION95
2.1045-2.2670.21181400.14482655X-RAY DIFFRACTION96
2.267-2.49510.21841570.15572669X-RAY DIFFRACTION98
2.4951-2.8560.2261490.16112718X-RAY DIFFRACTION99
2.856-3.59790.24681210.15722793X-RAY DIFFRACTION99
3.5979-37.6880.19981560.17052890X-RAY DIFFRACTION100
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDMethodL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
1refined1.1855-0.2714-0.36630.7991-0.34080.7307-0.00640.0348-0.16170.0203-0.0181-0.01240.145-0.04250.02180.1002-0.0226-0.00570.0835-0.00420.124-5.00338.247121.8802
20.54780.0769-0.35420.85130.0430.8103-0.03830.07430.0331-0.03490.05660.03230.0027-0.1336-0.01490.0684-0.0219-0.00560.09240.00740.0803
Refinement TLS groupSelection details: chain B

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