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Basic information

Entry
Database: PDB / ID: 4euk
TitleCrystal structure
Components
  • Histidine kinase 5
  • Histidine-containing phosphotransfer protein 1
KeywordsSIGNALING PROTEIN / multistep phosphorelay / two-component system / plant signalling / signal transduction / sensor histidine kinase / phosphotransfer protein / response regulator / TRANSFERASE
Function / homology
Function and homology information


negative regulation of abscisic acid-activated signaling pathway / negative regulation of ethylene-activated signaling pathway / multidimensional cell growth / embryo sac development / cellular response to molecule of bacterial origin / protein histidine kinase binding / regulation of stomatal closure / cytokinin-activated signaling pathway / ethylene-activated signaling pathway / histidine phosphotransfer kinase activity ...negative regulation of abscisic acid-activated signaling pathway / negative regulation of ethylene-activated signaling pathway / multidimensional cell growth / embryo sac development / cellular response to molecule of bacterial origin / protein histidine kinase binding / regulation of stomatal closure / cytokinin-activated signaling pathway / ethylene-activated signaling pathway / histidine phosphotransfer kinase activity / root development / protein histidine kinase activity / vacuole / abscisic acid-activated signaling pathway / histidine kinase / phosphorelay sensor kinase activity / plasma membrane => GO:0005886 / phosphorelay signal transduction system / cellular response to nitric oxide / defense response / cellular response to hydrogen peroxide / protein autophosphorylation / phosphorylation / metal ion binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
HPT domain / Hpt domain / Histidine-containing phosphotransfer (HPt) domain profile. / Signal transduction histidine kinase, phosphotransfer (Hpt) domain / HPT domain superfamily / 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 ...HPT domain / Hpt domain / Histidine-containing phosphotransfer (HPt) domain profile. / Signal transduction histidine kinase, phosphotransfer (Hpt) domain / HPT domain superfamily / 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 / Response regulator / Four Helix Bundle (Hemerythrin (Met), subunit A) / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / PAS domain superfamily / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Histidine kinase 5 / Histidine-containing phosphotransfer protein 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.95 Å
AuthorsStehle, T. / Bauer, J.
CitationJournal: Mol Plant / Year: 2013
Title: Structure-Function Analysis of Arabidopsis thaliana Histidine Kinase AHK5 Bound to Its Cognate Phosphotransfer Protein AHP1.
Authors: Bauer, J. / Reiss, K. / Veerabagu, M. / Heunemann, M. / Harter, K. / Stehle, T.
History
DepositionApr 25, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 20, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _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: Histidine kinase 5
B: Histidine-containing phosphotransfer protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0594
Polymers34,9732
Non-polymers862
Water3,279182
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1890 Å2
ΔGint-17 kcal/mol
Surface area14560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.800, 106.800, 106.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11B-315-

HOH

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Components

#1: Protein Histidine kinase 5 / / Arabidopsis histidine kinase 5 / AtHK5 / Protein AUTHENTIC HIS-KINASE 5 / Protein CYTOKININ-INDEPENDENT 2


Mass: 16928.432 Da / Num. of mol.: 1 / Fragment: Response regulatory domain, UNP residues 774-922
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: AHK5, At5g10720, CKI2, MAJ23.80 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 (DE3) / References: UniProt: Q3S4A7, histidine kinase
#2: Protein Histidine-containing phosphotransfer protein 1


Mass: 18044.486 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: AHP1, At3g21510, ATHP3, MIL23.8 / Plasmid: pGEX-6P1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 (DE3) / References: UniProt: Q9ZNV9
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 182 / 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: 2.9 Å3/Da / Density % sol: 57.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 20% PEG 550 MME, 10% PEG 20000, 0.1M MES/imidazole, 0.02M 1,6-hexanediol, 0.02M 1-butanol, 0.02M (R,S)-1,2-propandiol, 0.02M 2-propanol, 0.02M 1,3-propandiol, 0.02M 1,4-butandiol , pH 6.5, ...Details: 20% PEG 550 MME, 10% PEG 20000, 0.1M MES/imidazole, 0.02M 1,6-hexanediol, 0.02M 1-butanol, 0.02M (R,S)-1,2-propandiol, 0.02M 2-propanol, 0.02M 1,3-propandiol, 0.02M 1,4-butandiol , pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 19, 2011
RadiationMonochromator: Bartels monochromator (DCCM) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→47.76 Å / Num. all: 29841 / Num. obs: 29820 / % possible obs: 99.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 13.4 % / Biso Wilson estimate: 40.6 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 23.3
Reflection shellResolution: 1.95→2 Å / Redundancy: 11.2 % / Rmerge(I) obs: 0.413 / Mean I/σ(I) obs: 3.9 / Num. unique all: 2189 / % possible all: 99.4

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Processing

Software
NameVersionClassification
RemDAqdata collection
autoSHARPphasing
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: SIRAS / Resolution: 1.95→47.76 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.959 / SU B: 5.459 / SU ML: 0.08 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.125 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19683 1490 5 %RANDOM
Rwork0.17219 ---
all0.17342 29817 --
obs0.17342 28327 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.135 Å2
Refinement stepCycle: LAST / Resolution: 1.95→47.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2221 0 5 182 2408
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222326
X-RAY DIFFRACTIONr_bond_other_d0.0010.021524
X-RAY DIFFRACTIONr_angle_refined_deg1.2481.9663165
X-RAY DIFFRACTIONr_angle_other_deg0.87933789
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9345313
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.46726.476105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.4315432
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.046157
X-RAY DIFFRACTIONr_chiral_restr0.0740.2377
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022605
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02413
X-RAY DIFFRACTIONr_mcbond_it2.21251476
X-RAY DIFFRACTIONr_mcbond_other1.0995592
X-RAY DIFFRACTIONr_mcangle_it3.36852393
X-RAY DIFFRACTIONr_scbond_it5.05910850
X-RAY DIFFRACTIONr_scangle_it7.48710758
LS refinement shellResolution: 1.95→2.002 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 108 -
Rwork0.24 2063 -
obs-2175 100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
13.8117-2.51460.84132.3742-0.41611.5761-0.2885-0.4413-0.03260.44040.21650.04990.0157-0.13480.0720.18130.05730.01260.0948-0.00140.005510.09327.44540.961
22.4286-1.53260.09652.9152-0.05782.48260.16510.0460.0751-0.0819-0.2167-0.01530.18780.20550.05160.11410.0456-0.00930.0519-0.01870.043110.14528.83830.516
34.7239-1.930.13742.34010.891.1396-0.1908-0.23430.3330.12260.2872-0.38090.04610.0534-0.09640.14190.04350.00210.096-0.10190.17344.32151.92235.456
412.2821-0.84110.3910.70140.96831.65630.36010.07680.0086-0.06220.0432-0.3515-0.1002-0.0218-0.40330.14660.02390.0010.0899-0.11270.36024.33856.92135.115
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A776 - 859
2X-RAY DIFFRACTION2A860 - 922
3X-RAY DIFFRACTION3B1 - 101
4X-RAY DIFFRACTION4B102 - 152

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