+Open data
-Basic information
Entry | Database: PDB / ID: 7et5 | ||||||
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Title | Crystal structure of Arabidopsis TEM1 AP2 domain | ||||||
Components | AP2/ERF and B3 domain-containing transcription repressor TEM1 | ||||||
Keywords | DNA 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 | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.052 Å | ||||||
Authors | Hu, H. / Du, J. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7et5.cif.gz | 74.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7et5.ent.gz | 53.7 KB | Display | PDB format |
PDBx/mmJSON format | 7et5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7et5_validation.pdf.gz | 428.3 KB | Display | wwPDB validaton report |
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Full document | 7et5_full_validation.pdf.gz | 432.9 KB | Display | |
Data in XML | 7et5_validation.xml.gz | 7.2 KB | Display | |
Data in CIF | 7et5_validation.cif.gz | 9.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/et/7et5 ftp://data.pdbj.org/pub/pdb/validation_reports/et/7et5 | HTTPS FTP |
-Related structure data
Related structure data | 7et4C 7et6C 1gccS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | 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 |
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#2: Chemical | ChemComp-SO4 / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.68 Å3/Da / Density % sol: 26.67 % |
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Crystal grow | Temperature: 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 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 30, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 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
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 63.73 Å2 / Biso mean: 20.1632 Å2 / Biso min: 8.43 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.052→33.958 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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