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Open data
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Basic information
Entry | Database: PDB / ID: 6r0m | ||||||
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Title | Histone fold domain of AtNF-YB2/NF-YC3 in P212121 | ||||||
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![]() | TRANSCRIPTION / NF-Y / Transcription factor / arabidopsis | ||||||
Function / homology | ![]() 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 / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription cis-regulatory region binding / protein heterodimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / nucleus Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Chaves-Sanjuan, A. / Gnesutta, N. / Chiara, M. / Bernardini, A. / Fornara, F. / Horner, D. / Nardini, M. / Mantovani, R. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 159.3 KB | Display | ![]() |
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PDB format | ![]() | 126.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6r0lC ![]() 6r0nC ![]() 6r2vC ![]() 5g49S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 11160.813 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein | Mass: 11126.929 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.8 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 30% PEG 3350, 0.1 M MES pH 6.5 and 0.3 M lithium citrate |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 3, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.010876 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→44.07 Å / Num. obs: 20843 / % possible obs: 99.9 % / Redundancy: 12.7 % / Biso Wilson estimate: 47.1 Å2 / CC1/2: 0.998 / Net I/σ(I): 12.5 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 13.5 % / Mean I/σ(I) obs: 3.6 / Num. unique obs: 2054 / CC1/2: 0.575 / Rpim(I) all: 0.215 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5G49 Resolution: 2.3→44.07 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.924 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.265 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.276 / SU Rfree Blow DPI: 0.21 / SU Rfree Cruickshank DPI: 0.209
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Displacement parameters | Biso mean: 63.91 Å2
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Refine analyze | Luzzati coordinate error obs: 0.33 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.3→44.07 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.42 Å / Rfactor Rfree error: 0 / Total num. of bins used: 10
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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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