+Open data
-Basic information
Entry | Database: PDB / ID: 6r0n | ||||||
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Title | Histone fold domain of AtNF-YB2/NF-YC3 in I2 | ||||||
Components |
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Keywords | TRANSCRIPTION / NF-Y / Transcription factor / arabidopsis | ||||||
Function / homology | Function and homology information positive regulation of photomorphogenesis / long-day photoperiodism, flowering / CCAAT-binding factor complex / gibberellic acid mediated signaling pathway / regulation of seed germination / response to water deprivation / abscisic acid-activated signaling pathway / plastid / transcription coregulator activity / DNA-binding transcription activator activity, RNA polymerase II-specific ...positive regulation of photomorphogenesis / long-day photoperiodism, flowering / CCAAT-binding factor complex / gibberellic acid mediated signaling pathway / regulation of seed germination / response to water deprivation / abscisic acid-activated signaling pathway / plastid / transcription coregulator activity / DNA-binding transcription activator activity, RNA polymerase II-specific / sequence-specific DNA binding / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein heterodimerization activity / DNA-binding transcription factor activity / DNA binding / nucleus Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Chaves-Sanjuan, A. / Gnesutta, N. / Bernardini, A. / Fornara, F. / Nardini, M. / Mantovani, R. | ||||||
Citation | Journal: Plant J. / Year: 2021 Title: Structural determinants for NF-Y subunit organization and NF-Y/DNA association in plants. Authors: Chaves-Sanjuan, A. / Gnesutta, N. / Gobbini, A. / Martignago, D. / Bernardini, A. / Fornara, F. / Mantovani, R. / Nardini, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6r0n.cif.gz | 98.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6r0n.ent.gz | 67.2 KB | Display | PDB format |
PDBx/mmJSON format | 6r0n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r0/6r0n ftp://data.pdbj.org/pub/pdb/validation_reports/r0/6r0n | HTTPS FTP |
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-Related structure data
Related structure data | 6r0lC 6r0mC 6r2vC 5g49S 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 11160.813 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: AXX17_At5g46140 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A178UPH7, UniProt: Q9FGJ3*PLUS | ||||
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#2: Protein | Mass: 11126.929 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: AXX17_At1g49320 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A178WGU5, UniProt: Q9ZVL3*PLUS | ||||
#3: Chemical | #4: 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: 2.31 Å3/Da / Density % sol: 46.8 % |
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Crystal grow | Temperature: 277 K / Method: microdialysis / pH: 8 / Details: 100 mM NaCl, 50 mM Tris-HCl pH 8.0 and 2 mM DTT |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.999996 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 25, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.999996 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→49.4 Å / Num. obs: 11924 / % possible obs: 99.6 % / Observed criterion σ(I): 2.3 / Redundancy: 6.7 % / Biso Wilson estimate: 46.9 Å2 / CC1/2: 1 / Rpim(I) all: 0.018 / Net I/σ(I): 13.9 |
Reflection shell | Resolution: 2.1→2.16 Å / Redundancy: 6.8 % / Mean I/σ(I) obs: 2.3 / Num. unique obs: 958 / CC1/2: 0.86 / Rpim(I) all: 0.351 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5G49 Resolution: 2.1→49.35 Å / SU ML: 0.2136 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 30.1963 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 70.11 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→49.35 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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