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- PDB-7c1i: Crystal structure of histidine-containing phosphotransfer protein... -

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Basic information

Entry
Database: PDB / ID: 7c1i
TitleCrystal structure of histidine-containing phosphotransfer protein B (HptB) from Pseudomonas aeruginosa PAO1
ComponentsHistidine kinase
KeywordsTRANSFERASE / P. aeruginosa / Two-component regulatory system / Sensor histidine kinase / Histidine-containing phosphotransfer protein
Function / homology
Function and homology information


negative regulation of single-species biofilm formation / protein histidine kinase binding / histidine phosphotransfer kinase activity / positive regulation of chemotaxis / regulation of cell motility / phosphorelay signal transduction system / kinase activity / cytoplasm
Similarity search - Function
HPT domain / Hpt domain / Histidine-containing phosphotransfer (HPt) domain profile. / Signal transduction histidine kinase, phosphotransfer (Hpt) domain / HPT domain superfamily / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Histidine kinase / HPt domain-containing protein
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.58 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 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
B: Histidine kinase
C: Histidine kinase
D: Histidine kinase
E: Histidine kinase
F: Histidine kinase


Theoretical massNumber of molelcules
Total (without water)79,2186
Polymers79,2186
Non-polymers00
Water22,1401229
1
A: Histidine kinase
B: Histidine kinase
C: Histidine kinase


Theoretical massNumber of molelcules
Total (without water)39,6093
Polymers39,6093
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Histidine kinase
E: Histidine kinase
F: Histidine kinase


Theoretical massNumber of molelcules
Total (without water)39,6093
Polymers39,6093
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)119.172, 119.172, 171.950
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11C-238-

HOH

21E-401-

HOH

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Components

#1: Protein
Histidine kinase / Histidine-containing phosphotransfer (HPt) domain protein / Hpt domain-containing protein


Mass: 13202.974 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Gene: C0044_25200, F3H14_21835, GNQ12_19260, GNQ27_08460, NCTC10662_05262
Production host: Escherichia coli (E. coli) / References: UniProt: A0A2V3FJP9, UniProt: Q9HYQ0*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1229 / 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

Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: PEG 6000, bicine/sodium hydroxide

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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: Apr 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.58→50 Å / Num. obs: 166104 / % possible obs: 98.4 % / Redundancy: 14.5 % / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.02 / Rrim(I) all: 0.075 / Net I/σ(I): 36.3
Reflection shellResolution: 1.58→1.64 Å / Redundancy: 14.3 % / Rmerge(I) obs: 0.761 / Mean I/σ(I) obs: 4.2 / Num. unique obs: 16599 / Rpim(I) all: 0.208 / Rrim(I) all: 0.789 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MAD / Resolution: 1.58→29.37 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.954 / SU B: 1.577 / SU ML: 0.055 / Cross valid method: THROUGHOUT / ESU R: 0.076 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22542 8321 5 %RANDOM
Rwork0.19284 ---
obs0.19447 157637 98.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.963 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2--0.02 Å20 Å2
3----0.05 Å2
Refinement stepCycle: 1 / Resolution: 1.58→29.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5499 0 0 1229 6728
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0010.0136547
X-RAY DIFFRACTIONr_bond_other_d00.0176037
X-RAY DIFFRACTIONr_angle_refined_deg3.0851.6468924
X-RAY DIFFRACTIONr_angle_other_deg1.8041.58214002
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0865873
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.1920467
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.363151216
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.4531599
X-RAY DIFFRACTIONr_chiral_restr0.1290.2790
X-RAY DIFFRACTIONr_gen_planes_refined0.0180.028018
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021601
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_it2.9721.9293240
X-RAY DIFFRACTIONr_mcbond_other2.9391.9273239
X-RAY DIFFRACTIONr_mcangle_it3.7462.8624194
X-RAY DIFFRACTIONr_mcangle_other3.7632.8634195
X-RAY DIFFRACTIONr_scbond_it5.2032.4983307
X-RAY DIFFRACTIONr_scbond_other5.2032.4993308
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.2083.5544730
X-RAY DIFFRACTIONr_long_range_B_refined9.97627.6938564
X-RAY DIFFRACTIONr_long_range_B_other9.76525.868129
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.58→1.621 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 618 -
Rwork0.262 11651 -
obs--99.51 %

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