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- PDB-5wx9: Crystal Structure of AtERF96 with GCC-box -

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Basic information

Entry
Database: PDB / ID: 5wx9
TitleCrystal Structure of AtERF96 with GCC-box
Components
  • (GCC-box motif) x 2
  • Ethylene-responsive transcription factor ERF096
KeywordsDNA BINDING PROTEIN/DNA / Protein-DNA complex / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


positive regulation of cellular defense response / stomatal closure / positive regulation of abscisic acid-activated signaling pathway / ethylene-activated signaling pathway / sequence-specific DNA binding / DNA-binding transcription factor activity / positive regulation of DNA-templated transcription / nucleus
Similarity search - Function
Ethylene-responsive transcription factor / AP2/ERF domain superfamily / AP2/ERF domain profile. / DNA-binding domain in plant proteins such as APETALA2 and EREBPs / AP2/ERF domain / AP2 domain / DNA-binding domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / Ethylene-responsive transcription factor ERF096
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsChen, C.Y. / Cheng, Y.S.
CitationJournal: Plant Mol.Biol. / Year: 2020
Title: Structural insights into Arabidopsis ethylene response factor 96 with an extended N-terminal binding to GCC box.
Authors: Chen, C.Y. / Lin, P.H. / Chen, K.H. / Cheng, Y.S.
History
DepositionJan 6, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 22, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 18, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 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
A: Ethylene-responsive transcription factor ERF096
B: GCC-box motif
C: GCC-box motif


Theoretical massNumber of molelcules
Total (without water)21,0743
Polymers21,0743
Non-polymers00
Water6,089338
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3800 Å2
ΔGint-15 kcal/mol
Surface area11470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.976, 81.181, 38.999
Angle α, β, γ (deg.)90.00, 120.04, 90.00
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Ethylene-responsive transcription factor ERF096


Mass: 14364.763 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: ERF096, At5g43410, MWF20.11 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9LSX0
#2: DNA chain GCC-box motif


Mass: 3319.175 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Production host: synthetic construct (others)
#3: DNA chain GCC-box motif


Mass: 3390.209 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Production host: synthetic construct (others)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 338 / 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: 2.53 Å3/Da / Density % sol: 51.47 % / Mosaicity: 0.633 ° / Mosaicity esd: 0.01 °
Crystal growTemperature: 297 K / Method: vapor diffusion / pH: 7
Details: 0.02M Magnesium chloride hexahydrate &, 0.05M MOPS pH 7.0 &, 55% Tacsimate pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.97622 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 25, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97622 Å / Relative weight: 1
ReflectionResolution: 1.76→50 Å / Num. obs: 20152 / % possible obs: 97.3 % / Redundancy: 3.4 % / Biso Wilson estimate: 9.01 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 14.3
Reflection shellResolution: 1.76→1.82 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.341 / % possible all: 98.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data collection
SCALEPACKdata scaling
DENZOdata reduction
PDB_EXTRACT3.22data extraction
PHASERphasing
PHENIX1.9model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GCC

1gcc


Resolution: 1.76→21.12 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 18.05
RfactorNum. reflection% reflection
Rfree0.225 2005 10.04 %
Rwork0.206 --
obs0.208 19971 96.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 19.18 Å2
Refinement stepCycle: LAST / Resolution: 1.76→21.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1008 445 0 338 1791
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0141525
X-RAY DIFFRACTIONf_angle_d1.7732139
X-RAY DIFFRACTIONf_dihedral_angle_d27.295596
X-RAY DIFFRACTIONf_chiral_restr0.078219
X-RAY DIFFRACTIONf_plane_restr0.043207
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7641-1.80820.14151380.11481238X-RAY DIFFRACTION96
1.8082-1.85710.14081490.10941322X-RAY DIFFRACTION98
1.8571-1.91170.12791420.10621327X-RAY DIFFRACTION100
1.9117-1.97340.11851450.12531295X-RAY DIFFRACTION98
1.9734-2.04380.15551460.13561343X-RAY DIFFRACTION98
2.0438-2.12560.2321500.13721246X-RAY DIFFRACTION99
2.1256-2.22220.14731440.14661319X-RAY DIFFRACTION99
2.2222-2.33920.19141430.17191301X-RAY DIFFRACTION98
2.3392-2.48560.18151420.20531304X-RAY DIFFRACTION99
2.4856-2.67720.2281480.24261285X-RAY DIFFRACTION97
2.6772-2.94590.2621460.26341293X-RAY DIFFRACTION96
2.9459-3.37070.25911490.21731247X-RAY DIFFRACTION95
3.3707-4.24110.29361330.27651227X-RAY DIFFRACTION91
4.2411-21.11870.33811300.30391219X-RAY DIFFRACTION89

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