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- PDB-3mm4: Crystal structure of the receiver domain of the histidine kinase ... -

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Basic information

Entry
Database: PDB / ID: 3mm4
TitleCrystal structure of the receiver domain of the histidine kinase CKI1 from Arabidopsis thaliana
ComponentsHistidine kinase homolog
KeywordsTRANSFERASE / receiver domain / CKI1 / Arabidopsis / cytokinin signaling / Rossmann-fold / CheY-like
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
Histidine kinase CKI1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMarek, J. / Klumpler, T. / Pekarova, B. / Triskova, O. / Horak, J. / Zidek, L. / Dopitova, R. / Hejatko, J. / Janda, L.
Citation
Journal: Plant J. / Year: 2011
Title: Structure and binding specificity of the receiver domain of sensor histidine kinase CKI1 from Arabidopsis thaliana.
Authors: Pekarova, B. / Klumpler, T. / Triskova, O. / Horak, J. / Jansen, S. / Dopitova, R. / Borkovcova, P. / Papouskova, V. / Nejedla, E. / Sklenar, V. / Marek, J. / Zidek, L. / Hejatko, J. / Janda, L.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2009
Title: Cloning, purification, crystallization and preliminary X-ray analysis of the receiver domain of the histidine kinase CKI1 from Arabidopsis thaliana.
Authors: Klumpler, T. / Pekarova, B. / Marek, J. / Borkovcova, P. / Janda, L. / Hejatko, J.
History
DepositionApr 19, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 14, 2011Group: Database references
Revision 1.3Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histidine kinase homolog


Theoretical massNumber of molelcules
Total (without water)23,2261
Polymers23,2261
Non-polymers00
Water2,378132
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.458, 99.825, 79.943
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 homolog / Histidine kinase


Mass: 23225.879 Da / Num. of mol.: 1 / Fragment: Receiver Domain (UNP Residues 944-1122)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: cki1, At2g47430 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: O22267
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / 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: 2.34 Å3/Da / Density % sol: 47.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.05
Details: 0.1M MES, 2.54M Ammonium sulfate, pH 5.05, vapor diffusion, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8423 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 18, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8423 Å / Relative weight: 1
ReflectionResolution: 2→5 Å / Num. all: 15054 / Num. obs: 13674 / % possible obs: 98.3 % / Observed criterion σ(I): 2 / Redundancy: 11.1 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 15.8
Reflection shellResolution: 2→2.043 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.296 / % possible all: 75.9

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0102refinement
PDB_EXTRACT3.1data extraction
MAR345dtbdata collection
XDSdata reduction
XDSdata scaling
MrBUMPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AB5 (CheY)

1ab5


Resolution: 2→5 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.917 / Occupancy max: 1 / Occupancy min: 0.44 / SU B: 3.106 / SU ML: 0.091 / Cross valid method: THROUGHOUT / ESU R: 0.143 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2288 706 5 %RANDOM
Rwork0.17582 ---
obs0.17852 13322 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.605 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å20 Å2
2--0.02 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 2→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1133 0 0 132 1265
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0330.0221173
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.2541.9921571
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0035143
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.61624.65558
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.21315238
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0941511
X-RAY DIFFRACTIONr_chiral_restr0.210.2177
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021864
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.6921.5719
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.8121165
X-RAY DIFFRACTIONr_scbond_it4.5923454
X-RAY DIFFRACTIONr_scangle_it7.6714.5406
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.043 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.192 53 -
Rwork0.187 871 -
obs--100 %

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