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- PDB-8xat: Crystal structure of AtARR1(RD-DBD) -

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Basic information

Entry
Database: PDB / ID: 8xat
TitleCrystal structure of AtARR1(RD-DBD)
ComponentsTwo-component response regulator ARR1
KeywordsDNA BINDING PROTEIN / cytokinin / phosphorelay / B-ARR
Function / homology
Function and homology information


cellular response to cytokinin stimulus / regulation of cytokinin-activated signaling pathway / regulation of seed growth / callus formation / primary root development / regulation of anthocyanin metabolic process / maintenance of shoot apical meristem identity / axillary shoot meristem initiation / shoot system development / regulation of root meristem growth ...cellular response to cytokinin stimulus / regulation of cytokinin-activated signaling pathway / regulation of seed growth / callus formation / primary root development / regulation of anthocyanin metabolic process / maintenance of shoot apical meristem identity / axillary shoot meristem initiation / shoot system development / regulation of root meristem growth / response to cytokinin / regulation of chlorophyll biosynthetic process / cytokinin-activated signaling pathway / root development / response to water deprivation / phosphorelay response regulator activity / transcription cis-regulatory region binding / DNA-binding transcription factor activity / nucleus / cytosol
Similarity search - Function
Response regulator B-type, plant / Two-component response regulator ARR-like / Myb domain, plants / Myb-type HTH DNA-binding domain profile. / Myb domain / Myb-like DNA-binding domain / SANT/Myb domain / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain ...Response regulator B-type, plant / Two-component response regulator ARR-like / Myb domain, plants / Myb-type HTH DNA-binding domain profile. / Myb domain / Myb-like DNA-binding domain / SANT/Myb domain / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Homeobox-like domain superfamily
Similarity search - Domain/homology
Two-component response regulator ARR1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.205 Å
AuthorsLi, J.X. / Zhou, C.M. / Zhang, P. / Wang, J.W.
Funding support China, 4items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32388201 China
National Natural Science Foundation of China (NSFC)31721001 China
National Natural Science Foundation of China (NSFC)32025020 China
National Natural Science Foundation of China (NSFC)31870720 China
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2024
Title: The structure of B-ARR reveals the molecular basis of transcriptional activation by cytokinin.
Authors: Zhou, C.M. / Li, J.X. / Zhang, T.Q. / Xu, Z.G. / Ma, M.L. / Zhang, P. / Wang, J.W.
History
DepositionDec 5, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 24, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Two-component response regulator ARR1
B: Two-component response regulator ARR1


Theoretical massNumber of molelcules
Total (without water)66,5372
Polymers66,5372
Non-polymers00
Water6,089338
1
A: Two-component response regulator ARR1

A: Two-component response regulator ARR1


Theoretical massNumber of molelcules
Total (without water)66,5372
Polymers66,5372
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Buried area1960 Å2
ΔGint-10 kcal/mol
Surface area19340 Å2
MethodPISA
2
B: Two-component response regulator ARR1

B: Two-component response regulator ARR1


Theoretical massNumber of molelcules
Total (without water)66,5372
Polymers66,5372
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-x-1,y,-z1
Buried area1480 Å2
ΔGint-13 kcal/mol
Surface area20200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.108, 136.158, 141.057
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Two-component response regulator ARR1


Mass: 33268.652 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: ARR1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q940D0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 338 / 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: 2.64 Å3/Da / Density % sol: 53.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 2.0 M ammonium sulfate, 2% (v/v) Polyethylene Glycol (PEG) 400, 0.1 M HEPES, pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9798 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 2.205→36.554 Å / Num. obs: 35713 / % possible obs: 100 % / Redundancy: 13.2 % / Rmerge(I) obs: 0.112 / Net I/σ(I): 21
Reflection shellResolution: 2.205→2.284 Å / Rmerge(I) obs: 0.424 / Num. unique obs: 3409

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8XAS

8xas


Resolution: 2.205→36.554 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 21.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2231 1996 5.59 %
Rwork0.1913 --
obs0.193 35682 99.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.205→36.554 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3025 0 0 338 3363
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0193075
X-RAY DIFFRACTIONf_angle_d1.5724141
X-RAY DIFFRACTIONf_dihedral_angle_d24.3461195
X-RAY DIFFRACTIONf_chiral_restr0.108484
X-RAY DIFFRACTIONf_plane_restr0.007516
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.205-2.25980.27341340.21552239X-RAY DIFFRACTION94
2.2598-2.32090.26231430.20842385X-RAY DIFFRACTION99
2.3209-2.38910.22391370.20082372X-RAY DIFFRACTION100
2.3891-2.46620.27311400.19322391X-RAY DIFFRACTION100
2.4662-2.55440.25951450.20152413X-RAY DIFFRACTION100
2.5544-2.65660.2171360.19992388X-RAY DIFFRACTION100
2.6566-2.77750.23291470.20032402X-RAY DIFFRACTION100
2.7775-2.92390.271470.21052406X-RAY DIFFRACTION100
2.9239-3.1070.23281410.20062399X-RAY DIFFRACTION100
3.107-3.34670.22031430.19172430X-RAY DIFFRACTION100
3.3467-3.68320.21211500.17972421X-RAY DIFFRACTION100
3.6832-4.21550.18681390.16082441X-RAY DIFFRACTION100
4.2155-5.30850.17331440.16222474X-RAY DIFFRACTION100
5.3085-36.5540.24631500.22842525X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: -36.7028 Å / Origin y: -22.0661 Å / Origin z: -20.9931 Å
111213212223313233
T0.195 Å20.0526 Å2-0.0706 Å2-0.2145 Å2-0.0328 Å2--0.201 Å2
L0.9058 °20.3398 °2-0.3651 °2-0.9584 °20.0042 °2--0.7143 °2
S0.1564 Å °0.0396 Å °-0.0537 Å °0.0834 Å °-0.0774 Å °-0.1429 Å °-0.0594 Å °-0.1185 Å °-0.0794 Å °
Refinement TLS groupSelection details: all

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