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- PDB-4zds: Crystal Structure of core DNA binding domain of Arabidopsis Thali... -

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Basic information

Entry
Database: PDB / ID: 4zds
TitleCrystal Structure of core DNA binding domain of Arabidopsis Thaliana Transcription Factor Ethylene-Insensitive 3
ComponentsProtein ETHYLENE INSENSITIVE 3
KeywordsTRANSCRIPTION ACTIVATOR / DNA binding domain Transcription factor
Function / homology
Function and homology information


regulation of L-ascorbic acid biosynthetic process / sugar mediated signaling pathway / response to ethylene / ethylene-activated signaling pathway / epigenetic regulation of gene expression / kinase binding / histone binding / response to hypoxia / transcription cis-regulatory region binding / defense response to bacterium ...regulation of L-ascorbic acid biosynthetic process / sugar mediated signaling pathway / response to ethylene / ethylene-activated signaling pathway / epigenetic regulation of gene expression / kinase binding / histone binding / response to hypoxia / transcription cis-regulatory region binding / defense response to bacterium / DNA-binding transcription factor activity / chromatin binding / regulation of DNA-templated transcription / DNA binding / nucleus
Similarity search - Function
DNA-binding domain of ethylene- insensitive3-like3 / DNA-binding domain of EIN3-like / Ethylene insensitive 3 / Ethylene insensitive 3-like protein, DNA-binding domain superfamily / : / Ethylene insensitive 3, DNA-binding domain / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Protein ETHYLENE INSENSITIVE 3
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.78 Å
AuthorsSong, J. / Zhu, C. / Zhang, X. / Wen, X. / Liu, L. / Peng, J. / Guo, H. / Yi, C.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31270838 China
CitationJournal: Plos One / Year: 2015
Title: Biochemical and Structural Insights into the Mechanism of DNA Recognition by Arabidopsis ETHYLENE INSENSITIVE3.
Authors: Song, J. / Zhu, C. / Zhang, X. / Wen, X. / Liu, L. / Peng, J. / Guo, H. / Yi, C.
History
DepositionApr 18, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 23, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Data collection / Derived calculations / Category: diffrn_detector / pdbx_struct_oper_list
Item: _diffrn_detector.detector / _pdbx_struct_oper_list.symmetry_operation
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 ETHYLENE INSENSITIVE 3
B: Protein ETHYLENE INSENSITIVE 3


Theoretical massNumber of molelcules
Total (without water)30,7022
Polymers30,7022
Non-polymers00
Water2,540141
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.022, 45.174, 47.571
Angle α, β, γ (deg.)89.46, 77.07, 71.38
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Protein ETHYLENE INSENSITIVE 3


Mass: 15350.781 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 174-306 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: O24606
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.55 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1M HEPES, 25% w/v Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 2, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.78→46.26 Å / Num. obs: 23591 / % possible obs: 96.63 % / Redundancy: 3.9 % / Net I/σ(I): 22.81

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
DENZOdata reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 1.78→46.26 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.95 / SU B: 5.833 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.125 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21806 1270 5.1 %RANDOM
Rwork0.17419 ---
obs0.17652 23591 96.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.883 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å20.48 Å20.02 Å2
2--0.4 Å2-0.52 Å2
3----0.25 Å2
Refinement stepCycle: LAST / Resolution: 1.78→46.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2103 0 0 141 2244
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0192176
X-RAY DIFFRACTIONr_bond_other_d0.0010.022127
X-RAY DIFFRACTIONr_angle_refined_deg2.1261.9742962
X-RAY DIFFRACTIONr_angle_other_deg0.99334949
X-RAY DIFFRACTIONr_dihedral_angle_1_deg16.9725261
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.56324.65988
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.8815393
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.5311510
X-RAY DIFFRACTIONr_chiral_restr0.1250.2315
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.0212367
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02451
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.9612.2341044
X-RAY DIFFRACTIONr_mcbond_other1.9592.2341043
X-RAY DIFFRACTIONr_mcangle_it2.5323.3391302
X-RAY DIFFRACTIONr_mcangle_other2.5313.3391303
X-RAY DIFFRACTIONr_scbond_it3.4352.6811132
X-RAY DIFFRACTIONr_scbond_other3.4292.6791130
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.143.8331659
X-RAY DIFFRACTIONr_long_range_B_refined6.79819.0912607
X-RAY DIFFRACTIONr_long_range_B_other6.74318.8132560
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.781→1.827 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 85 -
Rwork0.279 1677 -
obs--91.58 %
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)
10.96070.25960.41591.5584-0.34641.65690.0528-0.0249-0.13010.0666-0.0313-0.01080.1196-0.1206-0.02160.0191-0.024-0.00280.0405-0.00050.019439.7703-11.847148.363
21.39080.1605-0.97191.10720.19462.69260.11130.15720.1473-0.03690.06320.0193-0.3143-0.1146-0.17450.04670.00970.01750.02240.01830.01932.74510.633527.1304
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A173 - 304
2X-RAY DIFFRACTION2B173 - 301

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