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- PDB-6kpb: The crystal structure of the JACKDAW/IDD10 bound to the homodimer... -

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Basic information

Entry
Database: PDB / ID: 6kpb
TitleThe crystal structure of the JACKDAW/IDD10 bound to the homodimeric SCL3
Components
  • Peptide from Zinc finger protein JACKDAW
  • Scarecrow-like protein 3
KeywordsTRANSCRIPTION / Transcription factor / asymmetric cell division / GRAS / IDD
Function / homology
Function and homology information


regulation of meristem growth / response to gibberellin / asymmetric cell division / root development / regulation of epidermal cell differentiation / regulation of cell division / protein localization to nucleus / sequence-specific DNA binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription ...regulation of meristem growth / response to gibberellin / asymmetric cell division / root development / regulation of epidermal cell differentiation / regulation of cell division / protein localization to nucleus / sequence-specific DNA binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / protein homodimerization activity / DNA binding / nucleus / metal ion binding
Similarity search - Function
Scarecrow-like protein 3 / : / Transcription factor GRAS / GRAS domain family / GRAS family profile. / Zinc finger, C2H2 type / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Zinc finger protein JACKDAW / Scarecrow-like protein 3
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsHirano, Y. / Hakoshima, T.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Science and TechnologyJPMJCR14M5 Japan
Japan Society for the Promotion of Science17K07448 Japan
CitationJournal: To Be Published
Title: Structure of the SCL3 homodimer bound to the BIRD/IDD transcription factor
Authors: Hirano, Y. / Shimizu, R. / Nishimura, T. / Morita, M.T. / Hakoshima, T.
History
DepositionAug 15, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 2, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 27, 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
C: Scarecrow-like protein 3
B: Peptide from Zinc finger protein JACKDAW
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,1703
Polymers56,0642
Non-polymers1061
Water362
1
C: Scarecrow-like protein 3
B: Peptide from Zinc finger protein JACKDAW
hetero molecules

C: Scarecrow-like protein 3
B: Peptide from Zinc finger protein JACKDAW
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,3406
Polymers112,1284
Non-polymers2122
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area4990 Å2
ΔGint-28 kcal/mol
Surface area33110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.037, 112.037, 70.979
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11C-501-

PEG

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Components

#1: Protein Scarecrow-like protein 3 / AtSCL3 / GRAS family protein 5 / AtGRAS-5


Mass: 54370.840 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: SCL3, At1g50420, F11F12.22 / Plasmid: pET49-b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9LPR8
#2: Protein/peptide Peptide from Zinc finger protein JACKDAW / ID1-like zinc finger protein 3 / Protein indeterminate-domain 10


Mass: 1692.975 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Arabidopsis thaliana (thale cress) / References: UniProt: Q700D2
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.29 Å3/Da / Density % sol: 46.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 2-5% 2-propanol, 0.05M tri-sodium citrate, 0.1M HEPES-NaOH (pH 7.0)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 15, 2018
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→48.51 Å / Num. obs: 20315 / % possible obs: 99.7 % / Redundancy: 4.6 % / CC1/2: 1 / Rmerge(I) obs: 0.017 / Rpim(I) all: 0.011 / Net I/σ(I): 21.8
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.631 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2115 / CC1/2: 0.9 / Rpim(I) all: 0.321 / % possible all: 100

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Processing

Software
NameClassification
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→43.9806 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflectionSelection details
Rfree0.214 1018 5.01 %Random selection
Rwork0.191 ---
obs0.1921 20315 99.53 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.4→43.9806 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3058 0 7 2 3067
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.52660.36761290.31032728X-RAY DIFFRACTION100
2.5266-2.68480.35211480.28362714X-RAY DIFFRACTION100
2.6848-2.89210.29891620.2462729X-RAY DIFFRACTION100
2.8921-3.18310.2391380.23032754X-RAY DIFFRACTION100
3.1831-3.64350.23231680.20362738X-RAY DIFFRACTION100
3.6435-4.58960.18531380.17292780X-RAY DIFFRACTION100
4.5896-43.98060.19481350.17722854X-RAY DIFFRACTION98
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)
12.2786-0.9467-0.63532.02860.39312.27790.14160.12680.1602-0.2935-0.22030.1932-0.10030.02490.07370.7057-0.0145-0.04070.67240.01420.640641.0649-17.2745-3.8865
23.2777-1.5137-3.53182.5731-1.5149.1461-0.34270.1917-0.77410.4781-0.82010.25690.0066-1.15891.11491.6829-0.4423-0.22372.069-0.09152.457924.3143-31.370711.1558
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain C and resid 45:482)C45 - 482
2X-RAY DIFFRACTION2(chain B and resid 369:382)B369 - 382

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