+Open data
-Basic information
Entry | Database: PDB / ID: 7c9p | ||||||
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Title | Crystal structure of rice histone-fold dimer GHD8/OsNF-YC2 | ||||||
Components |
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Keywords | TRANSCRIPTION / photoperiodic flowering / CCT family / NF-CCT complex / specific DNA recognition | ||||||
Function / homology | Function and homology information positive regulation of unidimensional cell growth / negative regulation of long-day photoperiodism, flowering / CCAAT-binding factor complex / flower development / DNA-binding transcription activator activity, RNA polymerase II-specific / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / protein heterodimerization activity / regulation of transcription by RNA polymerase II / regulation of DNA-templated transcription ...positive regulation of unidimensional cell growth / negative regulation of long-day photoperiodism, flowering / CCAAT-binding factor complex / flower development / DNA-binding transcription activator activity, RNA polymerase II-specific / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / protein heterodimerization activity / regulation of transcription by RNA polymerase II / regulation of DNA-templated transcription / DNA binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Oryza sativa Japonica Group (Japanese rice) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Shen, C. / Liu, H. / Guan, Z. / Xing, Y. / Yin, P. | ||||||
Citation | Journal: Plant Cell / Year: 2020 Title: Structural Insight into DNA Recognition by CCT/NF-YB/YC Complexes in Plant Photoperiodic Flowering. Authors: Shen, C. / Liu, H. / Guan, Z. / Yan, J. / Zheng, T. / Yan, W. / Wu, C. / Zhang, Q. / Yin, P. / Xing, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7c9p.cif.gz | 185.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7c9p.ent.gz | 122.8 KB | Display | PDB format |
PDBx/mmJSON format | 7c9p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7c9p_validation.pdf.gz | 452.2 KB | Display | wwPDB validaton report |
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Full document | 7c9p_full_validation.pdf.gz | 454.1 KB | Display | |
Data in XML | 7c9p_validation.xml.gz | 15.8 KB | Display | |
Data in CIF | 7c9p_validation.cif.gz | 21.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c9/7c9p ftp://data.pdbj.org/pub/pdb/validation_reports/c9/7c9p | HTTPS FTP |
-Related structure data
Related structure data | 7c9oSC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 10849.440 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryza sativa Japonica Group (Japanese rice) Gene: HD5, DTH8, GHD8, HAP3H, NFYB11, Os08g0174500, LOC_Os08g07740 Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q0J7P4 #2: Protein | Mass: 11907.627 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryza sativa Japonica Group (Japanese rice) Gene: NFYC2, HAP5C, Os03g0251350, LOC_Os03g14669 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A6BLW4 #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 40.16 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop Details: PEG 3350, sodium malonate, sodium citrate tribasic dihydrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97946 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 10, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 2→45 Å / Num. obs: 25020 / % possible obs: 99.7 % / Redundancy: 10.8 % / Biso Wilson estimate: 26.86 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.026 / Rrim(I) all: 0.086 / Net I/σ(I): 21.2 |
Reflection shell | Resolution: 2→2.05 Å / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 5.3 / Num. unique obs: 1825 / CC1/2: 0.918 / Rpim(I) all: 0.181 / Rrim(I) all: 0.608 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7C9O Resolution: 2→38.65 Å / SU ML: 0.1933 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 21.4282 / Stereochemistry target values: 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: 37.29 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→38.65 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -34.7707096507 Å / Origin y: 8.44159610158 Å / Origin z: 1.11804289245 Å
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Refinement TLS group | Selection details: all |