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- PDB-9c7n: Crystal Structure of the GL3 ACT-like Domain -

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Basic information

Entry
Database: PDB / ID: 9c7n
TitleCrystal Structure of the GL3 ACT-like Domain
ComponentsTranscription factor GLABRA 3
KeywordsLIPID BINDING PROTEIN / LBP / CRBPII
Function / homology
Function and homology information


positive regulation of anthocyanin biosynthetic process / trichome differentiation / trichome branching / jasmonic acid mediated signaling pathway / epidermal cell fate specification / cell fate specification / protein dimerization activity / DNA-binding transcription factor activity / DNA binding / nucleus
Similarity search - Function
: / Plant bHLH transcription factor, ACT-like domain / Transcription factor MYC/MYB N-terminal / bHLH-MYC and R2R3-MYB transcription factors N-terminal / Helix-loop-helix DNA-binding domain / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / Helix-loop-helix DNA-binding domain superfamily
Similarity search - Domain/homology
Transcription factor GLABRA 3
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsGhanbarpour, A. / Lee, Y.S. / Silwal, J. / Geiger, J.H. / Grotewold, E.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB-1822343 United States
National Science Foundation (NSF, United States)MCB-1513807 United States
CitationJournal: To Be Published
Title: Crystal Structure of the GL3 ACT-like Domain.
Authors: Ghanbarpour, A. / Lee, Y.S. / Silwal, J. / Geiger, J.H. / Grotewold, E.
History
DepositionJun 10, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 8, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcription factor GLABRA 3
B: Transcription factor GLABRA 3
C: Transcription factor GLABRA 3
D: Transcription factor GLABRA 3
E: Transcription factor GLABRA 3


Theoretical massNumber of molelcules
Total (without water)47,1155
Polymers47,1155
Non-polymers00
Water46826
1
A: Transcription factor GLABRA 3
E: Transcription factor GLABRA 3


Theoretical massNumber of molelcules
Total (without water)18,8462
Polymers18,8462
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1520 Å2
ΔGint-7 kcal/mol
Surface area8200 Å2
MethodPISA
2
B: Transcription factor GLABRA 3
C: Transcription factor GLABRA 3


Theoretical massNumber of molelcules
Total (without water)18,8462
Polymers18,8462
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1450 Å2
ΔGint-6 kcal/mol
Surface area8440 Å2
MethodPISA
3
D: Transcription factor GLABRA 3

D: Transcription factor GLABRA 3


Theoretical massNumber of molelcules
Total (without water)18,8462
Polymers18,8462
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556x,-y,-z+11
Buried area1380 Å2
ΔGint-9 kcal/mol
Surface area8660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.859, 83.524, 88.398
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein
Transcription factor GLABRA 3 / Basic helix-loop-helix protein 1 / AtMYC6 / AtbHLH1 / bHLH 1 / Protein SHAPESHIFTER / Transcription ...Basic helix-loop-helix protein 1 / AtMYC6 / AtbHLH1 / bHLH 1 / Protein SHAPESHIFTER / Transcription factor EN 31 / bHLH transcription factor bHLH001


Mass: 9422.913 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: GL3, BHLH1, EN31, MYC6, SST, At5g41315, MYC6.2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9FN69
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.62 Å3/Da / Density % sol: 53.04 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 150 mM NaCl, 10 mM Tris.HCl, 0.5 mM TCEP. HCl, pH:8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Nov 27, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.85→50 Å / Num. obs: 12015 / % possible obs: 99.3 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.092 / Rrim(I) all: 0.102 / Net I/σ(I): 6.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.85-2.95.60.7956120.7010.9080.3670.8780.797100
2.9-2.955.60.5915830.8430.9570.2710.6510.79100
2.95-3.015.50.5175850.860.9620.240.5720.785100
3.01-3.075.60.4165820.8960.9720.1920.460.83299.8
3.07-3.145.60.3545940.9330.9820.1630.3910.876100
3.14-3.215.50.2976020.9470.9860.1360.3280.87499.8
3.21-3.295.60.2535820.970.9920.1160.2790.915100
3.29-3.385.60.2056010.9790.9950.0940.2260.98399.7
3.38-3.485.50.1725960.9840.9960.0790.191.062100
3.48-3.595.60.1435880.9850.9960.0650.1581.0299.7
3.59-3.725.50.1285960.9840.9960.0590.1411.20499.5
3.72-3.875.60.1245910.9880.9970.0570.1371.364100
3.87-4.045.50.1135990.9880.9970.0520.1251.46499.5
4.04-4.265.50.0986040.9910.9980.0440.1081.4699.3
4.26-4.525.40.0785980.9930.9980.0360.0861.62899
4.52-4.875.50.0636130.9960.9990.0280.0691.36599.2
4.87-5.365.40.0556030.9960.9990.0260.0611.06599.2
5.36-6.145.40.0556070.9960.9990.0260.0610.88998.4
6.14-7.735.30.0486260.9980.9990.0230.0540.91898.4
7.73-504.80.0446530.9970.9990.0220.051.70495.2

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
HKL-2000data scaling
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.85→41.762 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2838 1207 10.07 %
Rwork0.2374 --
obs0.2421 11981 99.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.85→41.762 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2998 0 0 26 3024
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033035
X-RAY DIFFRACTIONf_angle_d0.7144103
X-RAY DIFFRACTIONf_dihedral_angle_d17.0861817
X-RAY DIFFRACTIONf_chiral_restr0.047497
X-RAY DIFFRACTIONf_plane_restr0.005516
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.85-2.9640.42281320.36471190X-RAY DIFFRACTION100
2.964-3.09890.36481280.30131175X-RAY DIFFRACTION100
3.0989-3.26220.35481400.28461173X-RAY DIFFRACTION100
3.2622-3.46650.30751260.27341193X-RAY DIFFRACTION100
3.4665-3.7340.27951400.23731171X-RAY DIFFRACTION100
3.734-4.10940.28971330.22361209X-RAY DIFFRACTION100
4.1094-4.70340.25491290.21192X-RAY DIFFRACTION99
4.7034-5.92310.25891390.21081215X-RAY DIFFRACTION99
5.9231-41.760.25861400.23211256X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: -39.3846 Å / Origin y: -8.9661 Å / Origin z: 17.2998 Å
111213212223313233
T0.3759 Å20.0006 Å20.0593 Å2-0.3162 Å20.022 Å2--0.4023 Å2
L1.0108 °20.1249 °20.7986 °2-1.3401 °20.2461 °2--1.8521 °2
S0.0133 Å °-0.0533 Å °-0.0249 Å °0.0289 Å °-0.059 Å °0.0943 Å °-0.0943 Å °-0.1181 Å °0.056 Å °
Refinement TLS groupSelection details: all

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