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- PDB-7c1j: Crystal structure of the receiver domain of sensor histidine kina... -

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Basic information

Entry
Database: PDB / ID: 7c1j
TitleCrystal structure of the receiver domain of sensor histidine kinase PA1611 (PA1611REC) from Pseudomonas aeruginosa PAO1 with magnesium ion coordinated in the active site cleft
ComponentsHistidine kinase
KeywordsTRANSFERASE / P. aeruginosa / Two-component regulatory system / Sensor histidine kinase / Histidine-containing phosphotransfer protein
Function / homology
Function and homology information


histidine phosphotransfer kinase activity / histidine kinase / phosphorelay sensor kinase activity / protein autophosphorylation / plasma membrane
Similarity search - Function
Histidine kinase BarA, N-terminal / Single cache domain 4 / 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 ...Histidine kinase BarA, N-terminal / Single cache domain 4 / 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. / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily
Similarity search - Domain/homology
Histidine kinase / histidine kinase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsChen, S.K. / Guan, H.H. / Wu, P.H. / Lin, L.T. / Wu, M.C. / Chang, H.Y. / Chen, N.C. / Lin, C.C. / Chuankhayan, P. / Huang, Y.C. ...Chen, S.K. / Guan, H.H. / Wu, P.H. / Lin, L.T. / Wu, M.C. / Chang, H.Y. / Chen, N.C. / Lin, C.C. / Chuankhayan, P. / Huang, Y.C. / Lin, P.J. / Chen, C.J.
CitationJournal: Iucrj / Year: 2020
Title: Structural insights into the histidine-containing phospho-transfer protein and receiver domain of sensor histidine kinase suggest a complex model in the two-component regulatory system in Pseudomonas aeruginosa
Authors: Chen, S.K. / Guan, H.H. / Wu, P.H. / Lin, L.T. / Wu, M.C. / Chang, H.Y. / Chen, N.C. / Lin, C.C. / Chuankhayan, P. / Huang, Y.C. / Lin, P.J. / Chen, C.J.
History
DepositionMay 4, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 4, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3162
Polymers18,2921
Non-polymers241
Water3,117173
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-8 kcal/mol
Surface area6290 Å2
Unit cell
Length a, b, c (Å)57.960, 57.960, 67.600
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-918-

HOH

21A-933-

HOH

31A-964-

HOH

41A-972-

HOH

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Components

#1: Protein Histidine kinase


Mass: 18291.627 Da / Num. of mol.: 1 / Fragment: receiver domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: barA_6, NCTC11839_05765 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A4U9SBT9, UniProt: Q9I3B1*PLUS, histidine kinase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 173 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.79 Å3/Da / Density % sol: 31.36 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: PEG 4000, MgCl2, Tris-HCl

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Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: May 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.35→30 Å / Num. obs: 28642 / % possible obs: 97.8 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.029 / Rrim(I) all: 0.075 / Net I/σ(I): 18.4
Reflection shellResolution: 1.35→1.4 Å / Redundancy: 6.3 % / Rmerge(I) obs: 1.255 / Mean I/σ(I) obs: 1.64 / Num. unique obs: 2862 / Rpim(I) all: 0.536 / Rrim(I) all: 1.368 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2R25

2r25


Resolution: 1.35→20.16 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.953 / SU B: 1.244 / SU ML: 0.049 / Cross valid method: THROUGHOUT / ESU R: 0.061 / ESU R Free: 0.066 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21637 1448 5.1 %RANDOM
Rwork0.18038 ---
obs0.18217 26942 96.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.59 Å2
Baniso -1Baniso -2Baniso -3
1-0.37 Å20.19 Å20 Å2
2--0.37 Å20 Å2
3----1.21 Å2
Refinement stepCycle: 1 / Resolution: 1.35→20.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms960 0 1 173 1134
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0131136
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171096
X-RAY DIFFRACTIONr_angle_refined_deg1.9451.6511552
X-RAY DIFFRACTIONr_angle_other_deg1.5371.5852526
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8595152
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.31219.02482
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.92215215
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2831521
X-RAY DIFFRACTIONr_chiral_restr0.0930.2144
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021379
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02280
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.572.232566
X-RAY DIFFRACTIONr_mcbond_other2.5422.229565
X-RAY DIFFRACTIONr_mcangle_it43.348732
X-RAY DIFFRACTIONr_mcangle_other43.352733
X-RAY DIFFRACTIONr_scbond_it3.2172.649570
X-RAY DIFFRACTIONr_scbond_other3.2152.648570
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.0133.823821
X-RAY DIFFRACTIONr_long_range_B_refined8.25630.2221407
X-RAY DIFFRACTIONr_long_range_B_other7.99928.6511343
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.351→1.386 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 98 -
Rwork0.305 2000 -
obs--99.34 %

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