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- PDB-4llc: The crystal structure of R60E mutant of the histidine kinase (Kin... -

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Basic information

Entry
Database: PDB / ID: 4llc
TitleThe crystal structure of R60E 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 / phosphatase activity / phosphorelay sensor kinase 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-related protein, C-terminal / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Histidine kinase domain / Histidine kinase domain profile. / PAS domain / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / PAS domain / PAS domain superfamily / Four Helix Bundle (Hemerythrin (Met), subunit A) / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / histidine kinase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsTan, K. / Chhor, G. / Jedrzejczak, R. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of R60E 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 1.2Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8328
Polymers29,0592
Non-polymers7736
Water1,04558
1
A: Probable two-component sensor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1806
Polymers14,5301
Non-polymers6515
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Probable two-component sensor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6522
Polymers14,5301
Non-polymers1221
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)84.651, 84.651, 73.974
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-302-

HOH

DetailsIt is predominantly a monomer in solution.

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Components

#1: Protein Probable two-component sensor


Mass: 14529.641 Da / Num. of mol.: 2 / Fragment: UNP residues 41-168 / Mutation: R60E
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-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.63 Å3/Da / Density % sol: 53.28 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2M magnesium chloride, 0.1M Tris-HCl, 30%(v/v) PEG400, pH 8.5, 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: 0.97929 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: 0.97929 Å / Relative weight: 1
ReflectionResolution: 2→37 Å / Num. all: 21023 / Num. obs: 21023 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -5 / Redundancy: 7.5 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 43.8
Reflection shellResolution: 2→2.03 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.551 / Mean I/σ(I) obs: 3.1 / Num. unique all: 1025 / % possible all: 100

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXDphasing
MLPHAREphasing
DMmodel building
ARPmodel building
WARPmodel building
HKL-3000phasing
PHENIX(phenix.refine: 1.7_650)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RefinementMethod to determine structure: SAD / Resolution: 2→36.655 Å / SU ML: 0.24 / σ(F): 0 / Phase error: 23.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2289 1026 5.08 %random
Rwork0.1947 ---
all0.1963 20191 --
obs0.1963 20191 95.61 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 57.826 Å2 / ksol: 0.393 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-7.8247 Å2-0 Å2-0 Å2
2--7.8247 Å20 Å2
3----15.6493 Å2
Refinement stepCycle: LAST / Resolution: 2→36.655 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1897 0 51 58 2006
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071967
X-RAY DIFFRACTIONf_angle_d0.9612649
X-RAY DIFFRACTIONf_dihedral_angle_d16.024755
X-RAY DIFFRACTIONf_chiral_restr0.06295
X-RAY DIFFRACTIONf_plane_restr0.003358
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.10420.29261140.22012416X-RAY DIFFRACTION85
2.1042-2.2360.2461500.19952607X-RAY DIFFRACTION93
2.236-2.40870.25861660.19082695X-RAY DIFFRACTION96
2.4087-2.6510.29581520.20472790X-RAY DIFFRACTION98
2.651-3.03440.2531620.20592817X-RAY DIFFRACTION99
3.0344-3.82240.221390.18492889X-RAY DIFFRACTION100
3.8224-36.66110.19371430.19242951X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 28.4034 Å / Origin y: 24.6727 Å / Origin z: 16.8776 Å
111213212223313233
T0.3016 Å20.0008 Å20.0122 Å2-0.3229 Å20.031 Å2--0.2817 Å2
L1.0572 °2-0.1026 °20.1866 °2-0.5055 °20.4025 °2--0.566 °2
S0.0388 Å °-0.2301 Å °-0.0602 Å °0.0932 Å °-0.0527 Å °-0.0355 Å °0.1529 Å °-0.0671 Å °0.0026 Å °
Refinement TLS groupSelection details: all

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