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- PDB-7p8e: Crystal structure of the Receiver domain of M. truncatula cytokin... -

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Basic information

Entry
Database: PDB / ID: 7p8e
TitleCrystal structure of the Receiver domain of M. truncatula cytokinin receptor MtCRE1
ComponentsReceiver domain of histidine kinase
KeywordsSIGNALING PROTEIN / flavodoxin-like fold / cytokinin / phosphorelay
Function / homology
Function and homology information


anatomical structure development / cytokinin-activated signaling pathway / histidine kinase / phosphorelay sensor kinase activity / membrane => GO:0016020 / hydrolase activity
Similarity search - Function
CHASE domain superfamily / CHASE domain / CHASE domain profile. / CHASE / CHASE 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 ...CHASE domain superfamily / CHASE domain / CHASE domain profile. / CHASE / CHASE 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 / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily
Similarity search - Domain/homology
Biological speciesMedicago truncatula (barrel medic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsTran, L.H. / Urbanowicz, A. / Jasinski, M. / Jaskolski, M. / Ruszkowski, M.
Funding support Poland, 1items
OrganizationGrant numberCountry
Polish National Science CentreSONATA 2018/31/D/NZ1/03630 Poland
CitationJournal: Front Plant Sci / Year: 2021
Title: 3D Domain Swapping Dimerization of the Receiver Domain of Cytokinin Receptor CRE1 From Arabidopsis thaliana and Medicago truncatula .
Authors: Tran, L.H. / Urbanowicz, A. / Jasinski, M. / Jaskolski, M. / Ruszkowski, M.
History
DepositionJul 21, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 20, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 2, 2022Group: Structure summary / Category: entity / Item: _entity.pdbx_description
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Receiver domain of histidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,3672
Polymers71,3261
Non-polymers401
Water543
1
A: Receiver domain of histidine kinase
hetero molecules

A: Receiver domain of histidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,7334
Polymers142,6532
Non-polymers802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area5240 Å2
ΔGint-76 kcal/mol
Surface area13500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.189, 60.189, 80.410
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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Components

#1: Protein Receiver domain of histidine kinase


Mass: 71326.422 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The sample was partially digested with thermolysin so only the receiver domain remained.
Source: (gene. exp.) Medicago truncatula (barrel medic) / Gene: 11411168, MTR_8g106150, MtrunA17_Chr8g0392301 / Production host: Escherichia coli (E. coli) / References: UniProt: G7LCC3, histidine kinase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.96 Å3/Da / Density % sol: 58.44 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Tris (base), BICINE pH 8.5 0.03 MgCl2, 0.03 CaCl2 12.5% MPD, 12.5% PEG1000, 12.5% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9755 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 9, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9755 Å / Relative weight: 1
ReflectionResolution: 2.5→52.2 Å / Num. obs: 3859 / % possible obs: 62.6 % / Redundancy: 6.2 % / Biso Wilson estimate: 67.43 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.042 / Rrim(I) all: 0.106 / Net I/σ(I): 12.9
Reflection shellResolution: 2.5→2.9 Å / Redundancy: 6 % / Rmerge(I) obs: 1.028 / Mean I/σ(I) obs: 2 / Num. unique obs: 296 / CC1/2: 0.78 / Rpim(I) all: 0.456 / Rrim(I) all: 1.129 / % possible all: 13.8

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Processing

Software
NameVersionClassification
PHENIX1.16_3546refinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EUK

4euk


Resolution: 2.5→52.125 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2212 191 4.95 %
Rwork0.1734 --
obs0.176 3859 62.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→52.125 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms992 0 1 3 996
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121010
X-RAY DIFFRACTIONf_angle_d1.1251355
X-RAY DIFFRACTIONf_dihedral_angle_d16.441613
X-RAY DIFFRACTIONf_chiral_restr0.054147
X-RAY DIFFRACTIONf_plane_restr0.008177
LS refinement shellResolution: 2.5→52.125 Å
RfactorNum. reflection% reflection
Rfree0.2212 191 -
Rwork0.1734 3668 -
obs--63 %
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)
14.6997-2.7205-3.04663.47641.22155.22220.3396-0.16150.2031-0.4284-0.3423-0.6722-0.69050.7071-0.06870.5349-0.10730.01180.34050.17980.416112.6736-1.4813-2.4465
27.6365.24170.68528.4639-3.20836.8826-0.56591.0606-1.5052-0.65950.23650.05431.6488-0.40730.33090.7546-0.14030.06290.4555-0.08260.8029-12.4215-2.23653.174
30.5502-0.4722-0.21930.6330.03210.1946-0.2517-0.110.02810.2506-0.0869-0.4621-0.25420.14180.08031.09360.1643-0.36890.42890.08991.1548.9845-24.097-2.5865
46.0843-0.2764-0.69565.16841.40247.07380.2066-0.9821-0.32550.761-0.3954-0.15720.63420.43220.21470.4314-0.1767-0.15840.56610.27160.451913.122-13.0486.8084
54.9847-2.5457-0.96964.88110.77733.10490.1854-0.50050.1146-0.0804-0.313-0.9517-0.31841.1925-0.21840.3668-0.1863-0.1210.64050.27970.705820.9538-7.5814-0.1228
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 920 through 971 )
2X-RAY DIFFRACTION2chain 'A' and (resid 972 through 994 )
3X-RAY DIFFRACTION3chain 'A' and (resid 856 through 861 )
4X-RAY DIFFRACTION4chain 'A' and (resid 862 through 892 )
5X-RAY DIFFRACTION5chain 'A' and (resid 893 through 919 )

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