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- PDB-3t4q: Arabidopsis histidine kinase 4 sensor domain in complex with tran... -

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Basic information

Entry
Database: PDB / ID: 3t4q
TitleArabidopsis histidine kinase 4 sensor domain in complex with trans-zeatin riboside (hydrolysed)
ComponentsHistidine kinase 4
Keywordshormone receptor / sensor histidine kinase / PAS domain / endoplasmic reticulum
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 / cellular response to sucrose stimulus / cytokinin-activated signaling pathway / protein histidine kinase binding / regulation of seed germination ...cytokinin receptor activity / transmembrane histidine kinase cytokinin receptor activity / embryonic root morphogenesis / regulation of shoot system development / regulation of meristem development / carbohydrate homeostasis / cellular response to sucrose stimulus / cytokinin-activated signaling pathway / protein histidine kinase binding / regulation of seed germination / sulfate transmembrane transport / protein histidine kinase activity / response to water deprivation / osmosensory signaling pathway / cellular response to phosphate starvation / protein-serine/threonine phosphatase / phosphorelay sensor kinase activity / histidine kinase / protein serine/threonine phosphatase activity / phosphorelay signal transduction system / phosphoprotein phosphatase activity / protein phosphorylation / defense response to bacterium / endoplasmic reticulum membrane / protein kinase binding / enzyme binding / endoplasmic reticulum / plasma membrane
Similarity search - Function
CHASE domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1190 / : / AHK4/CRE1/WOL first receiver domain / CHASE domain superfamily / CHASE domain / CHASE domain profile. / CHASE / CHASE domain / : ...CHASE domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1190 / : / AHK4/CRE1/WOL first receiver domain / CHASE domain superfamily / CHASE domain / CHASE domain profile. / CHASE / CHASE domain / : / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Phosphoribosyltransferase domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / Signal transduction histidine kinase-related protein, C-terminal / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / 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 / Beta-Lactamase / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Helix non-globular / Histidine kinase-like ATPases / Special / Histidine kinase/HSP90-like ATPase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
MALONATE ION / (2E)-2-methyl-4-(9H-purin-6-ylamino)but-2-en-1-ol / Histidine kinase 4
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsHothorn, M.
CitationJournal: Nat.Chem.Biol. / Year: 2011
Title: Structural basis for cytokinin recognition by Arabidopsis thaliana histidine kinase 4.
Authors: Hothorn, M. / Dabi, T. / Chory, J.
History
DepositionJul 26, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2011Group: Database references
Revision 1.2Jul 25, 2012Group: Other
Revision 1.3Sep 13, 2023Group: 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histidine kinase 4
B: Histidine kinase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,0125
Polymers61,4712
Non-polymers5413
Water7,782432
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3360 Å2
ΔGint-14 kcal/mol
Surface area25720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.900, 59.900, 297.440
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein 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: 30735.533 Da / Num. of mol.: 2 / Fragment: unp residues 149-418
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: AHK4, At2g01830, CRE1, RAW1, T23K3.2, WOL / Plasmid: pMH-HSsumo / Production host: Escherichia coli (E. coli) / Strain (production host): Origami (DE3)
References: UniProt: Q9C5U0, histidine kinase, protein-serine/threonine phosphatase
#2: Chemical ChemComp-ZEA / (2E)-2-methyl-4-(9H-purin-6-ylamino)but-2-en-1-ol / TRANS-ZEATIN


Mass: 219.243 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H13N5O
#3: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 432 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.51 Å3/Da / Density % sol: 50.92 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 16% PEG 3,350, 0.2 M Na malonate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 2, 2010 / Details: osmic mirrors
RadiationMonochromator: Co2+ Ka / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→29.36 Å / Num. all: 28135 / Num. obs: 28135 / % possible obs: 97.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Rsym value: 0.054 / Net I/σ(I): 14.9
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 5.27 / Num. unique all: 3227 / Rsym value: 0.198 / % possible all: 95.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7_650)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3T4J

3t4j


Resolution: 2.3→29.36 Å / SU ML: 0.31 / σ(F): 2.03 / Phase error: 21.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2369 1420 5.05 %RANDOM
Rwork0.1784 ---
obs0.1814 28132 97.95 %-
all-28135 --
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.832 Å2 / ksol: 0.342 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.6837 Å20 Å2-0 Å2
2--1.6837 Å2-0 Å2
3----3.3674 Å2
Refinement stepCycle: LAST / Resolution: 2.3→29.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4209 0 39 432 4680
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024496
X-RAY DIFFRACTIONf_angle_d0.5536110
X-RAY DIFFRACTIONf_dihedral_angle_d12.141719
X-RAY DIFFRACTIONf_chiral_restr0.043667
X-RAY DIFFRACTIONf_plane_restr0.002806
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2999-2.3820.28761350.19082496X-RAY DIFFRACTION95
2.382-2.47730.28781280.18912681X-RAY DIFFRACTION99
2.4773-2.590.2421560.18762660X-RAY DIFFRACTION99
2.59-2.72650.24761390.17852671X-RAY DIFFRACTION99
2.7265-2.89720.25431610.18122589X-RAY DIFFRACTION98
2.8972-3.12060.27061450.18252682X-RAY DIFFRACTION99
3.1206-3.43420.2761260.1822675X-RAY DIFFRACTION98
3.4342-3.93020.22321290.17652689X-RAY DIFFRACTION98
3.9302-4.94780.18821490.14922732X-RAY DIFFRACTION97
4.9478-29.36290.22431520.19672837X-RAY DIFFRACTION96
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)
10.05980.0071-0.02150.0431-0.00660.02570.0364-0.1325-0.04120.0325-0.12560.02830.0289-0.0073-0.01150.0346-0.02320.0510.34110.0380.0467-6.141813.149932.5227
20.171-0.0415-0.09520.02590.02440.0528-0.0150.0173-0.0113-0.0419-0.0644-0.0216-0.0558-0.0190.01190.02730.00760.00650.12980.02510.062710.130825.99612.9533
30.1821-0.02770.01230.0323-0.0110.02550.0623-0.0331-0.07910.0087-0.00150.0480.04740.05430.0401-0.0363-0.00950.03360.26130.00530.06086.39416.635224.3748
40.00890.0005-0.00710.00560.00020.01340.0287-0.0688-0.00230.0448-0.0579-0.0014-0.00470.005-0.01380.0818-0.04590.01190.37790.05950.06944.645413.388147.1787
50.0714-0.00220.01630.0610.04580.04160.0186-0.01940.01370.06230.0127-0.02440.03740.0091-0.01260.07370.0269-0.04990.25280.09140.0616-16.5801-0.285736.6683
60.0087-0.0080.00690.0083-0.00760.00740.00930.04190.0121-0.0254-0.0127-0.0062-0.01220.0034-0.00120.08840.05550.03160.21950.07640.127-14.112412.27788.9199
70.02920.01740.01440.01770.00260.00250.0313-0.0022-0.0189-0.0291-0.0094-0.01450.0016-0.06630.0021-0.27730.1347-0.1870.23480.0854-0.0042-29.40695.635910.0577
80.137-0.069-0.05880.081-0.00360.0520.02260.02220.08150.02150.041-0.0209-0.0285-0.0485-0.00140.04690.0201-0.03430.20990.06240.0929-28.40489.693320.6866
90.00130.00060.0020.0037-0.00130.0050.0180.0251-0.00490.0070.01430.0080.01650.0004-0.01660.18960.1064-0.04930.30240.02270.1378-16.0844-11.756731.6989
100.00940.0161-0.01920.0251-0.03290.1180.00320.0304-0.01330.00910.03860.01780.0006-0.0601-0.01650.13630.0130.00920.29160.02390.139-30.378-8.769336.9634
110.04550.00950.03530.03070.0030.03110.02120.02470.02970.02190.0021-0.005-0.0011-0.0157-0.0030.07310.0667-0.02680.17080.06460.0875-25.9052-4.160540.4586
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 126:197)
2X-RAY DIFFRACTION2chain 'A' and (resseq 198:244)
3X-RAY DIFFRACTION3chain 'A' and (resseq 245:334)
4X-RAY DIFFRACTION4chain 'A' and (resseq 335:393)
5X-RAY DIFFRACTION5chain 'B' and (resseq 127:171)
6X-RAY DIFFRACTION6chain 'B' and (resseq 172:190)
7X-RAY DIFFRACTION7chain 'B' and (resseq 191:272)
8X-RAY DIFFRACTION8chain 'B' and (resseq 273:323)
9X-RAY DIFFRACTION9chain 'B' and (resseq 324:341)
10X-RAY DIFFRACTION10chain 'B' and (resseq 342:370)
11X-RAY DIFFRACTION11chain 'B' and (resseq 371:393)

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