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- PDB-5b3g: The crystal structure of the heterodimer of SHORT-ROOT and SCAREC... -

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Basic information

Entry
Database: PDB / ID: 5b3g
TitleThe crystal structure of the heterodimer of SHORT-ROOT and SCARECROW GRAS domains
Components
  • Protein SCARECROW
  • Protein SHORT-ROOT
KeywordsTRANSCRIPTION / Transcription cofactor
Function / homology
Function and homology information


bundle sheath cell fate specification / radial pattern formation / regulation of hormone metabolic process / gravitropism / asymmetric cell division / leaf development / root development / maintenance of protein location in nucleus / negative regulation of mitotic cell cycle / cell redox homeostasis ...bundle sheath cell fate specification / radial pattern formation / regulation of hormone metabolic process / gravitropism / asymmetric cell division / leaf development / root development / maintenance of protein location in nucleus / negative regulation of mitotic cell cycle / cell redox homeostasis / recycling endosome / late endosome / sequence-specific DNA binding / early endosome / transcription cis-regulatory region binding / DNA-binding transcription factor activity / nucleus
Similarity search - Function
Transcription factor GRAS / GRAS domain family / GRAS family profile.
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / Protein SCARECROW / Protein SHORT-ROOT
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsHirano, Y. / Nakagawa, M. / Hakoshima, T.
Funding support Japan, 2items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology25440025 Japan
Ministry of Education, Culture, Sports, Science and Technology22121002 Japan
CitationJournal: Nat Plants / Year: 2017
Title: Structure of the SHR-SCR heterodimer bound to the BIRD/IDD transcriptional factor JKD
Authors: Hirano, Y. / Nakagawa, M. / Suyama, T. / Murase, K. / Shirakawa, M. / Takayama, S. / Sun, T.P. / Hakoshima, T.
History
DepositionFeb 29, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 1, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein SCARECROW
B: Protein SHORT-ROOT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,8489
Polymers95,2482
Non-polymers6007
Water5,152286
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5740 Å2
ΔGint-9 kcal/mol
Surface area31850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.700, 84.428, 89.797
Angle α, β, γ (deg.)90.00, 92.66, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Protein SCARECROW / AtSCR / GRAS family protein 20 / AtGRAS-20 / Protein SHOOT GRAVITROPISM 1


Mass: 42212.922 Da / Num. of mol.: 1 / Fragment: UNP residues 274-653
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: SCR, SGR1, At3g54220, F24B22.180 / Plasmid: pET47b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9M384
#2: Protein Protein SHORT-ROOT / AtSHR / GRAS family protein 26 / AtGRAS-26 / Protein SHOOT GRAVITROPISM 7


Mass: 53035.047 Da / Num. of mol.: 1 / Fragment: UNP residues 59-531
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: SHR, SGR7, At4g37650, F19F18.140 / Plasmid: pCDFDuet-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9SZF7

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Non-polymers , 4 types, 293 molecules

#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 286 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsSEQUENCE CONFLICT P233S IS BASED ON REFERENCE 4 (AAL69513) ACCORDING TO DATABASE Q9SZF7 (SHR_ARATH)

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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: 2.25 Å3/Da / Density % sol: 45.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: phosphate buffer (pH 7.0), polyethylene glycol (PEG) 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jan 26, 2011
RadiationMonochromator: Rotated-inclined double-crystal monochromator , Si (111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 56799 / % possible obs: 99.5 % / Redundancy: 3.7 % / Rsym value: 0.072 / Net I/σ(I): 28.1
Reflection shellResolution: 2→2.07 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 2→33.101 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 0.63 / Phase error: 23.8
RfactorNum. reflection% reflection
Rfree0.2296 2875 5.06 %
Rwork0.1835 --
obs0.1859 56799 99.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→33.101 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6069 0 38 286 6393
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076256
X-RAY DIFFRACTIONf_angle_d0.9788472
X-RAY DIFFRACTIONf_dihedral_angle_d14.4472266
X-RAY DIFFRACTIONf_chiral_restr0.055936
X-RAY DIFFRACTIONf_plane_restr0.0041097
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.03280.31111250.23772497X-RAY DIFFRACTION97
2.0328-2.06780.30591110.22482544X-RAY DIFFRACTION99
2.0678-2.10540.26731410.21412563X-RAY DIFFRACTION99
2.1054-2.14590.27261240.20512520X-RAY DIFFRACTION99
2.1459-2.18970.27221300.20542575X-RAY DIFFRACTION99
2.1897-2.23730.27861150.20712600X-RAY DIFFRACTION99
2.2373-2.28930.25511400.22272540X-RAY DIFFRACTION99
2.2893-2.34660.23681560.1892564X-RAY DIFFRACTION100
2.3466-2.410.23311450.18632571X-RAY DIFFRACTION100
2.41-2.48090.27251410.18982588X-RAY DIFFRACTION100
2.4809-2.56090.27391160.18982554X-RAY DIFFRACTION100
2.5609-2.65240.21251440.18732582X-RAY DIFFRACTION100
2.6524-2.75860.22451350.19792563X-RAY DIFFRACTION100
2.7586-2.88410.26421310.19282593X-RAY DIFFRACTION100
2.8841-3.0360.25391430.19922562X-RAY DIFFRACTION100
3.036-3.22610.23061460.20432583X-RAY DIFFRACTION100
3.2261-3.47490.20761310.18682584X-RAY DIFFRACTION100
3.4749-3.82420.21411530.16312598X-RAY DIFFRACTION100
3.8242-4.37640.21981410.1542581X-RAY DIFFRACTION100
4.3764-5.50970.19921480.15432599X-RAY DIFFRACTION100
5.5097-33.10590.20271590.17892563X-RAY DIFFRACTION97

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