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- PDB-4rqw: Crystal structure of Myc3 N-terminal JAZ-binding domain [44-238] ... -

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Basic information

Entry
Database: PDB / ID: 4rqw
TitleCrystal structure of Myc3 N-terminal JAZ-binding domain [44-238] from Arabidopsis
ComponentsTranscription factor MYC3
KeywordsTRANSCRIPTION REGULATOR / Helix-sheet-helix fold / Transcription factor / JAZ repressors / Nuclear
Function / homology
Function and homology information


extracellular ATP signaling / stomatal complex development / anthocyanin-containing compound biosynthetic process / response to jasmonic acid / bHLH transcription factor binding / defense response / protein dimerization activity / transcription cis-regulatory region binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription ...extracellular ATP signaling / stomatal complex development / anthocyanin-containing compound biosynthetic process / response to jasmonic acid / bHLH transcription factor binding / defense response / protein dimerization activity / transcription cis-regulatory region binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / nucleus
Similarity search - Function
Transcription factor AIB/MYC-like / Transcription factor MYC/MYB N-terminal / bHLH-MYC and R2R3-MYB transcription factors N-terminal / Helix-loop-helix DNA-binding domain / Helix-loop-helix DNA-binding domain superfamily / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile.
Similarity search - Domain/homology
Transcription factor MYC3
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsKe, J. / Zhang, F. / Zhou, X.E. / Brunzelle, J. / Zhou, M. / Xu, H.E. / Melcher, K. / He, S.Y.
CitationJournal: Nature / Year: 2015
Title: Structural basis of JAZ repression of MYC transcription factors in jasmonate signalling.
Authors: Zhang, F. / Yao, J. / Ke, J. / Zhang, L. / Lam, V.Q. / Xin, X.F. / Zhou, X.E. / Chen, J. / Brunzelle, J. / Griffin, P.R. / Zhou, M. / Xu, H.E. / Melcher, K. / He, S.Y.
History
DepositionNov 5, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 26, 2015Group: Database references
Revision 1.2Sep 16, 2015Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcription factor MYC3
B: Transcription factor MYC3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5374
Polymers43,4572
Non-polymers802
Water1,02757
1
A: Transcription factor MYC3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8083
Polymers21,7281
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Transcription factor MYC3


Theoretical massNumber of molelcules
Total (without water)21,7281
Polymers21,7281
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2330 Å2
ΔGint-31 kcal/mol
Surface area15290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.254, 76.619, 85.857
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.879841, -0.100293, 0.464566), (-0.088854, -0.994958, -0.046516), (0.466888, -0.000352, -0.884316)-4.42178, 97.68858, 37.4439

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Components

#1: Protein Transcription factor MYC3 / Basic helix-loop-helix protein 5 / AtbHLH5 / bHLH 5 / Protein altered tryptophan regulation 2 / ...Basic helix-loop-helix protein 5 / AtbHLH5 / bHLH 5 / Protein altered tryptophan regulation 2 / Transcription factor ATR2 / Transcription factor EN 36 / bHLH transcription factor bHLH005


Mass: 21728.309 Da / Num. of mol.: 2
Fragment: Myc3 N-terminal JAZ-binding domain (UNP residues 44-238)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At5g46760, ATR2, BHLH5, EN36, MYC3, MZA15.18 / Plasmid: pSUMO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9FIP9
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 57 / Source method: isolated from a natural source / Formula: H2O

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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: 2.17 Å3/Da / Density % sol: 43.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 25% (w/v) polyethylene glycol 3350, 0.2 M NaCl, 0.1 M Bis-Tris, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.9787 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 7, 2013
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 19813 / Num. obs: 19794 / % possible obs: 99.9 % / Redundancy: 8.2 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 20.6
Reflection shellResolution: 2.2→2.32 Å / % possible all: 100

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Processing

Software
NameVersionClassification
MD2programdata collection
AutoSolphasing
REFMAC5.7.0032refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.2→42.93 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.943 / SU B: 6.839 / SU ML: 0.171 / Cross valid method: THROUGHOUT / ESU R: 0.269 / ESU R Free: 0.22 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.26285 1012 5.1 %RANDOM
Rwork0.21447 ---
obs0.21688 18732 99.88 %-
all-18754 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 62.516 Å2
Baniso -1Baniso -2Baniso -3
1--0.72 Å2-0 Å20 Å2
2--0.44 Å2-0 Å2
3---0.28 Å2
Refinement stepCycle: LAST / Resolution: 2.2→42.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2546 0 2 57 2605
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0192592
X-RAY DIFFRACTIONr_angle_refined_deg1.2721.9313501
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0715322
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.16925.234128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.10615413
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.8471512
X-RAY DIFFRACTIONr_chiral_restr0.0820.2387
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021964
X-RAY DIFFRACTIONr_mcbond_it3.3896.0521309
X-RAY DIFFRACTIONr_mcangle_it5.2239.0261624
X-RAY DIFFRACTIONr_scbond_it4.1886.3281283
X-RAY DIFFRACTIONr_long_range_B_refined10.47356.64611017
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.348 66 -
Rwork0.307 1371 -
obs--100 %

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