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- PDB-7et5: Crystal structure of Arabidopsis TEM1 AP2 domain -

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Basic information

Entry
Database: PDB / ID: 7et5
TitleCrystal structure of Arabidopsis TEM1 AP2 domain
ComponentsAP2/ERF and B3 domain-containing transcription repressor TEM1
KeywordsDNA BINDING PROTEIN / GENE REGULATION / Flowering time regulation / plant protein
Function / homology
Function and homology information


photoperiodism, flowering / ethylene-activated signaling pathway / cellular response to hypoxia / transcription cis-regulatory region binding / DNA-binding transcription factor activity / nucleus
Similarity search - Function
B3 domain-containing transcription factor LEC2-like / AP2/ERF domain superfamily / AP2/ERF domain profile. / DNA-binding domain in plant proteins such as APETALA2 and EREBPs / AP2/ERF domain / B3 DNA binding domain / B3 DNA binding domain / B3 DNA-binding domain profile. / B3 DNA binding domain / DNA-binding pseudobarrel domain superfamily / DNA-binding domain superfamily
Similarity search - Domain/homology
AP2/ERF and B3 domain-containing transcription repressor TEM1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.052 Å
AuthorsHu, H. / Du, J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2021
Title: TEM1 combinatorially binds to FLOWERING LOCUS T and recruits a Polycomb factor to repress the floral transition in Arabidopsis.
Authors: Hu, H. / Tian, S. / Xie, G. / Liu, R. / Wang, N. / Li, S. / He, Y. / Du, J.
History
DepositionMay 12, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 15, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AP2/ERF and B3 domain-containing transcription repressor TEM1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9592
Polymers13,8631
Non-polymers961
Water2,162120
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-11 kcal/mol
Surface area6680 Å2
Unit cell
Length a, b, c (Å)37.650, 41.200, 59.966
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein AP2/ERF and B3 domain-containing transcription repressor TEM1 / Protein TEMPRANILLO 1 / RAV1-like ethylene-responsive transcription factor TEM1


Mass: 13863.179 Da / Num. of mol.: 1 / Fragment: AP2 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: TEM1, At1g25560, F2J7.3 / Plasmid: psumo / Production host: Escherichia coli (E. coli) / Strain (production host): DE3 / Variant (production host): rosetta / References: UniProt: Q9C6M5
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.68 Å3/Da / Density % sol: 26.67 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.2 M Li2SO4, 0.1 M Tris pH 8.5, 18% PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.05→50 Å / Num. obs: 42719 / % possible obs: 96.2 % / Redundancy: 6.2 % / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.022 / Rrim(I) all: 0.055 / Net I/σ(I): 24.2
Reflection shellResolution: 1.05→1.09 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.791 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 3611 / CC1/2: 0.644 / CC star: 0.885 / Rpim(I) all: 0.378 / Rrim(I) all: 0.881 / % possible all: 83

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GCC

1gcc


Resolution: 1.052→33.958 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 16.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1739 2078 4.87 %
Rwork0.1635 40591 -
obs0.1641 42669 96.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 63.73 Å2 / Biso mean: 20.1632 Å2 / Biso min: 8.43 Å2
Refinement stepCycle: final / Resolution: 1.052→33.958 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms810 0 5 120 935
Biso mean--11.39 27.06 -
Num. residues----99
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.0521-1.07660.2285102246188
1.0766-1.10350.23111350.211259294
1.1035-1.13330.21311220.1818264396
1.1333-1.16670.23131150.1806261895
1.1667-1.20440.20631580.1655265196
1.2044-1.24740.15541530.1495265097
1.2474-1.29740.15981250.1351270197
1.2974-1.35640.15961420.137267898
1.3564-1.42790.17351490.1385270998
1.4279-1.51740.17651360.1354272998
1.5174-1.63450.14751450.1361275399
1.6345-1.7990.15341450.1444277699
1.799-2.05930.17011560.15092794100
2.0593-2.59440.16721480.16272846100
2.5944-100.18191472990100

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