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- PDB-5lnm: Crystal structure of D1050E mutant of the receiver domain of the ... -

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Basic information

Entry
Database: PDB / ID: 5lnm
TitleCrystal structure of D1050E mutant of the receiver domain of the histidine kinase CKI1 from Arabidopsis thaliana
ComponentsHistidine kinase CKI1
KeywordsTRANSFERASE / receiver domain / mutant / histidine kinase CKI1 / (alpha/beta)5 fold
Function / homology
Function and homology information


secondary growth / phloem or xylem histogenesis / embryo sac development / cytokinin-activated signaling pathway / protein histidine kinase activity / plasmodesma / histidine kinase / phosphorelay sensor kinase activity / protein homodimerization activity / plasma membrane
Similarity search - Function
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 ...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 / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Histidine kinase CKI1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsOtrusinova, O. / Demo, G. / Kaderavek, P. / Jansen, S. / Jasenakova, Z. / Pekarova, B. / Janda, L. / Wimmerova, M. / Hejatko, J. / Zidek, L.
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Conformational dynamics are a key factor in signaling mediated by the receiver domain of a sensor histidine kinase from Arabidopsis thaliana.
Authors: Otrusinova, O. / Demo, G. / Padrta, P. / Jasenakova, Z. / Pekarova, B. / Gelova, Z. / Szmitkowska, A. / Kaderavek, P. / Jansen, S. / Zachrdla, M. / Klumpler, T. / Marek, J. / Hritz, J. / ...Authors: Otrusinova, O. / Demo, G. / Padrta, P. / Jasenakova, Z. / Pekarova, B. / Gelova, Z. / Szmitkowska, A. / Kaderavek, P. / Jansen, S. / Zachrdla, M. / Klumpler, T. / Marek, J. / Hritz, J. / Janda, L. / Iwai, H. / Wimmerova, M. / Hejatko, J. / Zidek, L.
History
DepositionAug 5, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 13, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Jul 17, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Jan 10, 2024Group: 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 CKI1


Theoretical massNumber of molelcules
Total (without water)23,2401
Polymers23,2401
Non-polymers00
Water1,69394
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.337, 98.728, 79.897
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Histidine kinase CKI1 / Protein CYTOKININ-INDEPENDENT 1


Mass: 23239.904 Da / Num. of mol.: 1 / Fragment: UNP residues 944-1122
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: CKI1, At2g47430, T30B22.27
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: O22267, histidine kinase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 94 / 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: 2.44 Å3/Da / Density % sol: 49.67 %
Crystal growTemperature: 290.15 K / Method: vapor diffusion, hanging drop / pH: 5.05 / Details: 2.54 M (NH4)2(SO4), 0.1 M MES pH 5.05

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 0.97522 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 6, 2009
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97522 Å / Relative weight: 1
ReflectionResolution: 1.95→47.6 Å / Num. obs: 15893 / % possible obs: 99.2 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.117 / Net I/σ(I): 10.8
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 4 % / Rmerge(I) obs: 0.665 / Mean I/σ(I) obs: 1.6 / % possible all: 94.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MM4

3mm4


Resolution: 1.95→42.37 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.934 / SU B: 3.96 / SU ML: 0.109 / Cross valid method: THROUGHOUT / ESU R: 0.174 / ESU R Free: 0.153 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23381 696 5 %RANDOM
Rwork0.20718 ---
obs0.20848 13110 86.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 34.402 Å2
Baniso -1Baniso -2Baniso -3
1-1.17 Å20 Å2-0 Å2
2--0.05 Å20 Å2
3----1.23 Å2
Refinement stepCycle: 1 / Resolution: 1.95→42.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1172 0 0 94 1266
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0191212
X-RAY DIFFRACTIONr_bond_other_d0.0020.021205
X-RAY DIFFRACTIONr_angle_refined_deg2.0371.9921621
X-RAY DIFFRACTIONr_angle_other_deg1.62532791
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6295148
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.11124.40759
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.35215249
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5021512
X-RAY DIFFRACTIONr_chiral_restr0.1070.2182
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021338
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02252
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_it3.3023.075598
X-RAY DIFFRACTIONr_mcbond_other3.2853.068597
X-RAY DIFFRACTIONr_mcangle_it4.7224.581744
X-RAY DIFFRACTIONr_mcangle_other4.7194.588745
X-RAY DIFFRACTIONr_scbond_it4.7023.638614
X-RAY DIFFRACTIONr_scbond_other4.6983.645615
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.3395.236878
X-RAY DIFFRACTIONr_long_range_B_refined9.00425.2621467
X-RAY DIFFRACTIONr_long_range_B_other8.97425.0841443
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.505 61 -
Rwork0.532 842 -
obs--78.05 %

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