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- PDB-5n2n: Crystal structure of the receiver domain of the histidine kinase ... -

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Basic information

Entry
Database: PDB / ID: 5n2n
TitleCrystal structure of the receiver domain of the histidine kinase CKI1 from Arabidopsis thaliana complexed with Mg2+ and BeF3-
ComponentsHistidine kinase CKI1
KeywordsTRANSFERASE / receiver domain / 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 / phosphorelay sensor kinase activity / histidine kinase / 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-related protein, C-terminal / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Histidine kinase domain / Histidine kinase domain profile. / Response regulator receiver domain / cheY-homologous receiver 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. / 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 superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
BERYLLIUM TRIFLUORIDE ION / Histidine kinase CKI1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsOtrusinova, O. / Demo, G. / Padrta, P. / Jasenakova, Z. / Pekarova, B. / Gelova, Z. / Szmitkowska, A. / Kaderavek, P. / Jansen, S. / Zachrdla, M. ...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.
Funding support Czech Republic, 1items
OrganizationGrant numberCountry
Czech Science FoundationGAP305/11/0756 Czech Republic
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
DepositionFeb 8, 2017Deposition 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 1.2Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
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.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histidine kinase CKI1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3163
Polymers23,2261
Non-polymers902
Water95553
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area350 Å2
ΔGint-6 kcal/mol
Surface area7650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.850, 100.152, 80.139
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-1342-

HOH

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Components

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


Mass: 23225.879 Da / Num. of mol.: 1
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: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: BeF3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 2.29 Å3/Da / Density % sol: 46.27 % / Description: prism
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.05
Details: 2.54 M (NH4)2(SO4), 0.1 M MES pH 5.05, 12% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 8, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.05→46.74 Å / Num. obs: 13705 / % possible obs: 99.9 % / Redundancy: 6.5 % / CC1/2: 1 / Rmerge(I) obs: 0.05 / Net I/σ(I): 20.5
Reflection shellResolution: 2.05→2.16 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 4.1 / CC1/2: 0.945 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MM4

3mm4


Resolution: 2.05→42.47 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.952 / SU B: 4.034 / SU ML: 0.11 / Cross valid method: THROUGHOUT / ESU R: 0.146 / ESU R Free: 0.144 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22515 658 4.8 %RANDOM
Rwork0.18175 ---
obs0.18378 13028 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 46.22 Å2
Baniso -1Baniso -2Baniso -3
1-3.23 Å20 Å2-0 Å2
2---0.15 Å20 Å2
3----3.08 Å2
Refinement stepCycle: 1 / Resolution: 2.05→42.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1160 0 5 53 1218
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0191182
X-RAY DIFFRACTIONr_bond_other_d0.0020.021136
X-RAY DIFFRACTIONr_angle_refined_deg1.851.9891573
X-RAY DIFFRACTIONr_angle_other_deg1.0232629
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0295147
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.17824.82156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.17815228
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.2731510
X-RAY DIFFRACTIONr_chiral_restr0.1580.2176
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021315
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02241
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_it4.1594.102594
X-RAY DIFFRACTIONr_mcbond_other4.154.098593
X-RAY DIFFRACTIONr_mcangle_it5.4796.123739
X-RAY DIFFRACTIONr_mcangle_other5.4786.128740
X-RAY DIFFRACTIONr_scbond_it6.2124.957588
X-RAY DIFFRACTIONr_scbond_other6.224.969583
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.3377.108832
X-RAY DIFFRACTIONr_long_range_B_refined11.28833.2821337
X-RAY DIFFRACTIONr_long_range_B_other11.30133.2381329
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 55 -
Rwork0.202 936 -
obs--100 %

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