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- PDB-4lle: The crystal structure of R60L mutant of the histidine kinase (Kin... -

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Basic information

Entry
Database: PDB / ID: 4lle
TitleThe crystal structure of R60L mutant of the histidine kinase (KinB) sensor domain from Pseudomonas aeruginosa PA01
ComponentsProbable two-component sensor
KeywordsTRANSFERASE / structural genomics / PSI-Biology / protein structure initiative / midwest center for structural genomics / MCSG
Function / homology
Function and homology information


histidine kinase / phosphorelay sensor kinase activity / phosphatase activity / 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. ...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
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 Å
AuthorsTan, K. / Chhor, G. / Jedrzejczak, R. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of R60L mutant of the histidine kinase (KinB) sensor domain from Pseudomonas aeruginosa PA01
Authors: Tan, K. / Chhor, G. / Jedrzejczak, R. / Joachimiak, A.
History
DepositionJul 9, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2013Group: Other
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable two-component sensor
B: Probable two-component sensor
C: Probable two-component sensor
D: Probable two-component sensor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,4238
Polymers58,0554
Non-polymers3684
Water3,963220
1
A: Probable two-component sensor
B: Probable two-component sensor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3045
Polymers29,0272
Non-polymers2763
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4970 Å2
ΔGint-56 kcal/mol
Surface area11670 Å2
MethodPISA
2
C: Probable two-component sensor
D: Probable two-component sensor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1193
Polymers29,0272
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4610 Å2
ΔGint-56 kcal/mol
Surface area11570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.235, 47.804, 49.422
Angle α, β, γ (deg.)75.98, 80.19, 74.54
Int Tables number1
Space group name H-MP1
DetailsThe mutant is in a mixture of monomer and dimer in solution. The dimer selectively crystallized.

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Components

#1: Protein
Probable two-component sensor


Mass: 14513.686 Da / Num. of mol.: 4 / Fragment: UNP residues 41-168 / Mutation: R60L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: PA5484 / Plasmid: pMCSG19B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: Q9HT87
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 220 / 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: 1.71 Å3/Da / Density % sol: 28.08 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.17M Ammonium acetate, 0.085M Sodium Acetate-HCl, 25.5% (w/v) PEG4000, 15% (v/v) Glycerol, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97928 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 2, 2011 / Details: mirror
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97928 Å / Relative weight: 1
ReflectionResolution: 1.68→35 Å / Num. all: 42068 / Num. obs: 42068 / % possible obs: 95.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -5 / Redundancy: 5 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 41
Reflection shellResolution: 1.68→1.71 Å / Redundancy: 5 % / Rmerge(I) obs: 0.518 / Mean I/σ(I) obs: 4 / Num. unique all: 2146 / % possible all: 95.9

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.7_650)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3KKB

3kkb


Resolution: 1.68→34.026 Å / SU ML: 0.22 / σ(F): 0.05 / Phase error: 23.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2419 2054 5.02 %random
Rwork0.196 ---
obs0.1983 40952 92.78 %-
all-40952 --
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 62.832 Å2 / ksol: 0.387 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.7236 Å2-0.3327 Å20.3125 Å2
2---2.0504 Å21.2676 Å2
3---0.3267 Å2
Refinement stepCycle: LAST / Resolution: 1.68→34.026 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3623 0 24 220 3867
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063808
X-RAY DIFFRACTIONf_angle_d0.9245163
X-RAY DIFFRACTIONf_dihedral_angle_d17.6151466
X-RAY DIFFRACTIONf_chiral_restr0.057588
X-RAY DIFFRACTIONf_plane_restr0.003708
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.68-1.71550.28471210.25522281X-RAY DIFFRACTION82
1.7155-1.75840.32431220.24852496X-RAY DIFFRACTION89
1.7584-1.80590.27391560.2372504X-RAY DIFFRACTION90
1.8059-1.85910.26421360.21782501X-RAY DIFFRACTION91
1.8591-1.91910.26651400.20772606X-RAY DIFFRACTION93
1.9191-1.98770.23781360.20162698X-RAY DIFFRACTION95
1.9877-2.06720.23911420.19292680X-RAY DIFFRACTION96
2.0672-2.16130.2431380.1912694X-RAY DIFFRACTION97
2.1613-2.27520.20871380.18182708X-RAY DIFFRACTION97
2.2752-2.41770.25021290.18382734X-RAY DIFFRACTION97
2.4177-2.60440.2191420.19242728X-RAY DIFFRACTION98
2.6044-2.86630.25291440.1942697X-RAY DIFFRACTION97
2.8663-3.28080.22231470.19112685X-RAY DIFFRACTION96
3.2808-4.13230.23251420.17342531X-RAY DIFFRACTION91
4.1323-34.03290.25841210.2172355X-RAY DIFFRACTION84
Refinement TLS params.Method: refined / Origin x: -4.7567 Å / Origin y: -4.5678 Å / Origin z: -23.823 Å
111213212223313233
T0.1282 Å20.0119 Å20.0143 Å2-0.142 Å2-0.012 Å2--0.1239 Å2
L0.3659 °20.3347 °20.2059 °2-1.81 °2-0.4893 °2--0.4153 °2
S-0.0082 Å °0.0229 Å °-0.0281 Å °-0.0905 Å °-0.0573 Å °-0.0716 Å °0.0325 Å °0.0208 Å °0.0102 Å °
Refinement TLS groupSelection details: all

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