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- PDB-8xas: Crystal structure of AtARR1-DBD in complex with a DNA fragment -

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Basic information

Entry
Database: PDB / ID: 8xas
TitleCrystal structure of AtARR1-DBD in complex with a DNA fragment
Components
  • (DNA (50-MER)) x 2
  • Two-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 / regulation of anthocyanin metabolic process / primary root development / maintenance of shoot apical meristem identity / axillary shoot meristem initiation / regulation of root meristem growth / shoot system development ...cellular response to cytokinin stimulus / regulation of cytokinin-activated signaling pathway / regulation of seed growth / callus formation / regulation of anthocyanin metabolic process / primary root development / maintenance of shoot apical meristem identity / axillary shoot meristem initiation / regulation of root meristem growth / shoot system development / 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
Two-component response regulator ARR-like / Response regulator B-type, plant / 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 ...Two-component response regulator ARR-like / Response regulator B-type, plant / 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
DNA / DNA (> 10) / Two-component response regulator ARR1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.346 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

Downloads & links

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Assembly

Deposited unit
A: Two-component response regulator ARR1
B: Two-component response regulator ARR1
C: Two-component response regulator ARR1
D: Two-component response regulator ARR1
E: Two-component response regulator ARR1
F: Two-component response regulator ARR1
X: DNA (50-MER)
G: DNA (50-MER)
Y: DNA (50-MER)
H: DNA (50-MER)


Theoretical massNumber of molelcules
Total (without water)86,05010
Polymers86,05010
Non-polymers00
Water4,936274
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.831, 79.112, 162.501
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Two-component response regulator ARR1


Mass: 9224.339 Da / Num. of mol.: 6
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: DNA chain DNA (50-MER)


Mass: 7584.949 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (50-MER)


Mass: 7767.042 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 274 / 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: 2.76 Å3/Da / Density % sol: 55.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M ammonium sulfate, 0.1 M sodium acetate trihydrate pH 4.6, 30% (w/v) PEG monomethyl ether 2000

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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: Feb 13, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 2.346→38.234 Å / Num. obs: 62499 / % possible obs: 99.7 % / Redundancy: 9 % / Rmerge(I) obs: 0.107 / Net I/σ(I): 20
Reflection shellResolution: 2.346→2.43 Å / Rmerge(I) obs: 1.8 / Num. unique obs: 2434

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.346→38.234 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2423 3424 5.48 %
Rwork0.1966 --
obs0.1991 62499 81.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.346→38.234 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2961 2050 0 274 5285
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0135311
X-RAY DIFFRACTIONf_angle_d1.2817604
X-RAY DIFFRACTIONf_dihedral_angle_d30.8622152
X-RAY DIFFRACTIONf_chiral_restr0.361868
X-RAY DIFFRACTIONf_plane_restr0.008609
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3463-2.37980.3724780.29061245X-RAY DIFFRACTION41
2.3798-2.41530.3098800.27721356X-RAY DIFFRACTION45
2.4153-2.45310.3139830.26831438X-RAY DIFFRACTION47
2.4531-2.49330.3328820.25021555X-RAY DIFFRACTION52
2.4933-2.53620.2637930.26041729X-RAY DIFFRACTION55
2.5362-2.58240.26321210.24171781X-RAY DIFFRACTION60
2.5824-2.6320.2879960.23441971X-RAY DIFFRACTION65
2.632-2.68570.28311340.22992119X-RAY DIFFRACTION71
2.6857-2.74410.29311240.23422365X-RAY DIFFRACTION77
2.7441-2.80790.25051460.25052342X-RAY DIFFRACTION78
2.8079-2.87810.28651440.25152614X-RAY DIFFRACTION86
2.8781-2.95590.28521800.23872768X-RAY DIFFRACTION91
2.9559-3.04290.29371660.23132803X-RAY DIFFRACTION93
3.0429-3.1410.25631630.22082904X-RAY DIFFRACTION96
3.141-3.25320.24931640.21172959X-RAY DIFFRACTION97
3.2532-3.38340.29731720.19733054X-RAY DIFFRACTION100
3.3834-3.53730.22491890.20023000X-RAY DIFFRACTION100
3.5373-3.72360.2191740.18163022X-RAY DIFFRACTION99
3.7236-3.95670.22551610.17543000X-RAY DIFFRACTION99
3.9567-4.26180.17891690.1583021X-RAY DIFFRACTION100
4.2618-4.690.21111800.14333054X-RAY DIFFRACTION100
4.69-5.36710.19931810.1623003X-RAY DIFFRACTION100
5.3671-6.75590.24581760.18733040X-RAY DIFFRACTION100
6.7559-38.2340.22391680.18362932X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: -17.2213 Å / Origin y: -20.2224 Å / Origin z: 6.7972 Å
111213212223313233
T0.1844 Å20.0009 Å2-0.0185 Å2-0.2295 Å20.0093 Å2--0.1999 Å2
L0.4487 °2-0.117 °2-0.116 °2-1.0197 °20.1579 °2--0.145 °2
S0.0191 Å °-0.0129 Å °-0.0175 Å °0.0328 Å °-0.029 Å °-0.0084 Å °-0.0107 Å °-0.0099 Å °0.0127 Å °
Refinement TLS groupSelection details: all

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