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- PDB-6kpd: The crystal structure of the BALDIBIS/IDD9 bound to the homodimer... -

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Basic information

Entry
Database: PDB / ID: 6kpd
TitleThe crystal structure of the BALDIBIS/IDD9 bound to the homodimeric SCL3
Components
  • Peptide from Zinc finger protein BALDIBIS
  • 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 / protein localization to nucleus / sequence-specific DNA binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / nucleus / metal ion binding
Similarity search - Function
: / BIRD-IDD transcription factor, fourth C2HC zinc finger / BIRD-IDD transcription factor, third C2HC zinc finger / BIRD-IDD transcription factor, second C2H2 zinc finger / Transcription factor GRAS / GRAS domain family / GRAS family profile. / Zinc finger, C2H2 type / zinc finger / Zinc finger C2H2 type domain profile. ...: / BIRD-IDD transcription factor, fourth C2HC zinc finger / BIRD-IDD transcription factor, third C2HC zinc finger / BIRD-IDD transcription factor, second C2H2 zinc finger / 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
Zinc finger protein BALDIBIS / Scarecrow-like protein 3
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsHirano, Y. / Shimizu, R. / 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 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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 BALDIBIS


Theoretical massNumber of molelcules
Total (without water)54,6772
Polymers54,6772
Non-polymers00
Water00
1
C: Scarecrow-like protein 3
B: Peptide from Zinc finger protein BALDIBIS

C: Scarecrow-like protein 3
B: Peptide from Zinc finger protein BALDIBIS


Theoretical massNumber of molelcules
Total (without water)109,3544
Polymers109,3544
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_765-x+2,-x+y+1,-z+2/31
Buried area4850 Å2
ΔGint-38 kcal/mol
Surface area33160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.384, 103.384, 68.690
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

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Components

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


Mass: 50824.766 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The sample sequence has the N-terminal additional residues (G-P, tag) and a deletion region corresponding to (270-301). These are genetically modified for the recombinant protein expression.
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: SCL3, At1g50420, F11F12.22 / Plasmid: pET49b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9LPR8
#2: Protein/peptide Peptide from Zinc finger protein BALDIBIS / ID1-like zinc finger protein 1 / Protein indeterminate-domain 9


Mass: 3852.378 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: BIB, IDD9, IDZ1, At3g45260, F18N11.20 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q944L3

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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: 1.94 Å3/Da / Density % sol: 36.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5
Details: PEG 3350, sodium sulfate, Bis-Tris propane-NaOH (pH 6.5)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 7, 2017
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: 3.2→44.77 Å / Num. obs: 7177 / % possible obs: 99.3 % / Redundancy: 4.2 % / CC1/2: 0.995 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.061 / Net I/σ(I): 6.7
Reflection shellResolution: 3.2→3.42 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.521 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 1279 / CC1/2: 0.701 / Rpim(I) all: 0.36 / % possible all: 99.1

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Processing

Software
NameClassification
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5B3G

5b3g


Resolution: 3.2→44.77 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflectionSelection details
Rfree0.2368 394 5.49 %Random selection
Rwork0.2037 ---
obs-7177 99.17 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.2→44.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3012 0 0 0 3012
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2005-3.66340.28611640.24722177X-RAY DIFFRACTION99
3.6634-4.61480.21891260.19312242X-RAY DIFFRACTION99
4.6148-44.770.21911040.19472364X-RAY DIFFRACTION100

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