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- PDB-7p8c: Crystal structure of the Receiver domain of A. thaliana cytokinin... -

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Basic information

Entry
Database: PDB / ID: 7p8c
TitleCrystal structure of the Receiver domain of A. thaliana cytokinin receptor AtCRE1 in complex with K+
ComponentsReceiver domain of histidine kinase 4
KeywordsSIGNALING PROTEIN / flavodoxin-like fold / cytokinin / phosphorelay
Function / homology
Function and homology information


cytokinin receptor activity / transmembrane histidine kinase cytokinin receptor activity / embryonic root morphogenesis / regulation of shoot system development / regulation of meristem development / carbohydrate homeostasis / regulation of seed germination / sulfate transport / cellular response to sucrose stimulus / protein histidine kinase binding ...cytokinin receptor activity / transmembrane histidine kinase cytokinin receptor activity / embryonic root morphogenesis / regulation of shoot system development / regulation of meristem development / carbohydrate homeostasis / regulation of seed germination / sulfate transport / cellular response to sucrose stimulus / protein histidine kinase binding / cytokinin-activated signaling pathway / protein histidine kinase activity / response to water deprivation / cellular response to phosphate starvation / osmosensory signaling pathway / myosin phosphatase activity / protein-serine/threonine phosphatase / histidine kinase / phosphorelay signal transduction system / phosphoprotein phosphatase activity / phosphorelay sensor kinase activity / defense response to bacterium / protein phosphorylation / endoplasmic reticulum membrane / protein kinase binding / enzyme binding / endoplasmic reticulum / plasma membrane
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 / Phosphoribosyltransferase domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily ...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 / Phosphoribosyltransferase 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
: / Histidine kinase 4
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 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

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Assembly

Deposited unit
A: Receiver domain of histidine kinase 4
B: Receiver domain of histidine kinase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0294
Polymers29,9512
Non-polymers782
Water73941
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3580 Å2
ΔGint-31 kcal/mol
Surface area15090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.319, 101.426, 33.549
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 916 through 1035 or resid 1118))
d_2ens_1chain "B"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ASNPHEA1 - 120
d_21ens_1ASNPHEC1 - 120

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Components

#1: Protein Receiver domain of histidine kinase 4 / Arabidopsis histidine kinase 4 / AtHK4 / Cytokinin receptor CYTOKININ RESPONSE 1 / AtCRE1 / ...Arabidopsis histidine kinase 4 / AtHK4 / Cytokinin receptor CYTOKININ RESPONSE 1 / AtCRE1 / Cytokinin receptor CRE1 / Phosphoprotein phosphatase AHK4 / Protein AUTHENTIC HIS-KINASE 4 / Protein ROOT AS IN WOL 1 / Protein WOODEN LEG


Mass: 14975.309 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: AHK4, CRE1, RAW1, WOL, At2g01830, T23K3.2 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9C5U0, histidine kinase, protein-serine/threonine phosphatase
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 41 / 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: 2.72 Å3/Da / Density % sol: 54.78 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1 M HEPES pH 7.0, 30% v/v Jeffamine M-600 pH 7.0

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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: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→41.25 Å / Num. obs: 10946 / % possible obs: 62.2 % / Redundancy: 12.9 % / Biso Wilson estimate: 37.72 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.176 / Rpim(I) all: 0.051 / Rrim(I) all: 0.184 / Net I/σ(I): 11.4
Reflection shellResolution: 2.15→2.39 Å / Redundancy: 11.5 % / Rmerge(I) obs: 1.23 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 544 / CC1/2: 0.73 / Rpim(I) all: 0.367 / Rrim(I) all: 1.286 / % possible all: 11.4

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Processing

Software
NameVersionClassification
MxCuBEdata collection
STARANISOdata scaling
XDSdata reduction
PHENIX1.18.2_3874refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EUK

4euk


Resolution: 2.15→41.25 Å / SU ML: 0.3247 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.4287
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2842 554 5 %
Rwork0.2086 10517 -
obs0.2124 10946 64.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.71 Å2
Refinement stepCycle: LAST / Resolution: 2.15→41.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1968 0 2 41 2011
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00882000
X-RAY DIFFRACTIONf_angle_d1.00912693
X-RAY DIFFRACTIONf_chiral_restr0.0549307
X-RAY DIFFRACTIONf_plane_restr0.0062345
X-RAY DIFFRACTIONf_dihedral_angle_d21.2211750
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 1.44789184932 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.380.346230.2742440X-RAY DIFFRACTION10.95
2.38-2.720.3239970.27231828X-RAY DIFFRACTION45.54
2.72-3.430.31182090.24073972X-RAY DIFFRACTION97.05
3.43-41.250.26382250.18474277X-RAY DIFFRACTION99.82
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)
14.453854178-5.590970608841.606783830117.02914533836-1.897661149382.44626917837-0.01197670231110.4083633016370.213153363725-1.00328533310.129934977365-1.081429435180.313360670376-0.169568878156-0.1313807957180.401790930582-0.07139154171310.07165505486830.389009377606-0.05534375989710.4756777448875.3232125603916.1412738971-1.6221284188
28.34751523034-0.190696654407-5.377353480364.271259507273.376966754655.969045108880.184352085434-0.974071678221-0.4984113575350.5471223203190.0218692806894-0.6733496198610.3301362407940.681812276481-0.2741771421650.5807510764170.0145026074482-0.05246828182470.2926038033670.1145687938380.3951105855949.7630211995822.25922444397.07025159698
33.83694323883-0.129454178145-3.105174970132.12078620894-2.163960592734.94305252141-0.477373846635-0.54548066421.48050877826-0.5653106141191.68043643292-0.62032671804-0.7817860132410.320247485623-0.5565208830890.527824992294-0.03735262507060.001610270153830.314602384868-0.1316244426290.60570438250910.977865266137.936911620919.1418771067
44.04751690424-1.340538030570.2118476699316.177217465861.588171474984.66361060056-0.136951984974-0.3583382587780.2297857639260.1621603952190.2382148152-0.21224634898-0.02586862498240.0944145481427-0.1322780084930.4747637657760.04488234660540.0389435051650.2611183205060.008542068930310.3314026401636.391481157223.03382864920.7325551848
53.09568450371-2.91370236718-2.312078946328.87796760714-2.264399582414.974328327440.4976032552450.4370360464960.8264771364470.6385336328860.4906821226532.62910415313-0.565218611787-1.99220712815-0.02980216789260.310278204436-0.1466982710880.1244982073960.3365057755630.004437323711390.375909507829-7.2789743170322.973861709716.8608696116
63.45144095488-0.979661723360.08188153249729.585322970870.2446417284832.26359676048-0.0841820471028-0.0402506440985-0.1630724115240.3305275710980.3621926792220.1799219970080.0771543808825-0.0931848392283-0.297623464350.26494099432-0.006286284135690.08302234554120.3118662319540.027252039210.257660252543-2.2598257403922.851107912613.4501804458
76.23782384601-4.47193063057-0.01819887971826.96370396804-0.2303561169054.28512880677-0.0164788732130.2601199462970.0510441205537-0.6143344133280.01901932140080.70188609140.0574227513408-1.024676589320.01617102835950.254382375360.0367420108406-0.01194057471330.4165348949010.02089862401920.369163841967-9.8886181707627.1369048215.81418502975
83.1544679416-3.456162556440.9731905383014.76476425467-0.5492212431554.30335190031-0.0225205427712-1.01993559780.488251143043-0.7377101971590.607910022269-0.0632720828166-0.425407412267-0.159836377894-0.2379852176460.3016235711570.07571050476510.006252103996820.2804771699030.02747584818210.345291154067-1.5627318165830.48580400057.55052645145
96.61106414844-1.54836451745-1.253956257448.798993063553.005703422688.510813479620.20251107675-0.2222115129570.6452609240680.454471350527-0.4674362515520.01712550847260.3285224050160.2483907103370.3487207463490.405285766532-0.02393340477490.02175497907920.3210649968210.0219854321890.33862199069513.38394000444.705424667077.53957465831
102.83176300913-0.6161063754392.898883933951.911120980880.9093711531844.36907150753-0.228262579256-0.2516299180420.695228941591-0.640185282578-0.4733889536210.212381774341-1.510435114030.04276575823930.5541839359810.3108723276910.125752876371-0.0395033414680.3268182691910.05996706226650.52543287460920.45449040287.00359917671-1.34682172132
114.925479094170.00169623359009-1.067515684346.87943239636-1.858362274344.736428603340.0948849685372-0.549634935765-0.498231654930.237104205354-0.170891788657-1.119163975460.6922469376130.7662988562650.1513208879320.4949601398440.0304028273370.01605913011910.439825631052-0.002773404449980.61784013145117.187836173222.8222825096-21.8619162342
128.132913560380.264748853313-1.173114475173.96234887864-1.775676194021.492068968130.154309545347-0.183655285484-0.7300666364470.149365669801-0.346658671483-0.231452647330.001842190086980.138376116050.2599147225790.335542724516-0.002265829694930.1069684128670.278030645361-0.03487176782730.27304021011625.72368009522.78096307022-11.9288856402
134.541076295090.1624425754570.03244004479962.07062648689-1.318080752993.05012151391-0.2358129685590.663240115435-0.352018686812-0.2923193158240.05682740544940.005463217420740.334898947205-0.07912875244010.1381323642850.307466414793-0.05941697059940.06921185745050.3176252548610.02698641152290.21894494874521.21229059725.28498186971-15.9980208588
146.38770978745-1.81362146838-0.4071715617666.845765351820.925001687475.075036481890.006293936386320.239938510804-0.462701329479-0.372181279702-0.1394876268240.1016508793180.0838794177164-0.006594646593880.1187138861130.28445456413-0.01261173461590.01746977905930.199907045061-0.00453454256750.19560064056717.1588795956-5.41969225819-8.91326134685
157.01315732216-4.755597789691.891667359498.926386853122.224240258163.46566488475-0.379498862432-0.924234404491-1.589671887080.04344434521880.3050011820470.7631510263520.740313082962-0.03650971946220.1188938440430.4478428825390.0393685226690.1564188181140.3421416401640.1084503272590.53599438061919.5175684688-13.0960915872-0.935804433393
168.61782139051-2.56417170912-0.9555669667480.912166327470.752618415951.49978683758-0.44301537468-1.727041097020.08438441411440.4805505451080.15596496155-1.350625963650.1863690933180.176886327715-0.08488292809860.4330833729650.1508279552410.1195462405560.3211211748950.05310282699370.39174129998128.847247101-11.7734387951-1.55733390233
173.67230500345-5.67281943383-0.7211986370069.020639326172.598126722947.26018644445-0.2061256191990.3131389205240.91588694963-0.1392958426960.698973380893-1.33681938277-1.16578420047-0.124652046934-0.1814102176840.1868675840810.05160948850690.1255851675630.2598846618310.05387868730990.30457038511118.7893529233.6471078322-2.94561729098
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'B' and (resid 1012 through 1025 )BC1012 - 102597 - 110
22chain 'B' and (resid 1026 through 1035 )BC1026 - 1035111 - 120
33chain 'A' and (resid 916 through 922 )AA916 - 9221 - 7
44chain 'A' and (resid 923 through 953 )AA923 - 9538 - 38
55chain 'A' and (resid 954 through 961 )AA954 - 96139 - 46
66chain 'A' and (resid 962 through 980 )AA962 - 98047 - 65
77chain 'A' and (resid 981 through 999 )AA981 - 99966 - 84
88chain 'A' and (resid 1000 through 1011 )AA1000 - 101185 - 96
99chain 'A' and (resid 1012 through 1025 )AA1012 - 102597 - 110
1010chain 'A' and (resid 1026 through 1035 )AA1026 - 1035111 - 120
1111chain 'A' and (resid 1036 through 1048 )AA1036 - 1048121 - 133
1212chain 'B' and (resid 916 through 930 )BC916 - 9301 - 15
1313chain 'B' and (resid 931 through 953 )BC931 - 95316 - 38
1414chain 'B' and (resid 954 through 980 )BC954 - 98039 - 65
1515chain 'B' and (resid 981 through 999 )BC981 - 99966 - 84
1616chain 'B' and (resid 1000 through 1006 )BC1000 - 100685 - 91
1717chain 'B' and (resid 1007 through 1011 )BC1007 - 101192 - 96

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