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- PDB-6r0l: Histone fold domain of OsGhd8/NF-YC7 in I2 -

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Basic information

Entry
Database: PDB / ID: 6r0l
TitleHistone fold domain of OsGhd8/NF-YC7 in I2
Components
  • OsGhd8
  • OsNF-YC7
KeywordsTRANSCRIPTION / NF-Y / Transcription factor / rice
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 / DNA binding ...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 / DNA binding / nucleus / cytoplasm
Similarity search - Function
Transcription factor, NFYB/HAP3, conserved site / Transcription factor NFYB/HAP3 / NF-YB/HAP3 subunit signature. / : / Transcription factor CBF/NF-Y/archaeal histone domain / Histone-like transcription factor (CBF/NF-Y) and archaeal histone / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold
Similarity search - Domain/homology
Os09g0480700 protein / Nuclear transcription factor Y subunit B-11 / Nuclear transcription factor Y subunit C-6
Similarity search - Component
Biological speciesOryza sativa (Asian cultivated rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsChaves-Sanjuan, A. / Gobbini, A. / Nardini, M.
CitationJournal: 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
DepositionMar 13, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 30, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 30, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 3, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.3Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: OsGhd8
B: OsNF-YC7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0834
Polymers18,8992
Non-polymers1842
Water73941
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5020 Å2
ΔGint-51 kcal/mol
Surface area8900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.836, 34.102, 67.081
Angle α, β, γ (deg.)90.00, 95.39, 90.00
Int Tables number5
Space group name H-MI121

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Components

#1: Protein OsGhd8 / OsNF-YB11 / Protein DAYS TO HEADING 8 / Protein HEADING DATE 5 / Transcriptional activator HAP3H / ...OsNF-YB11 / Protein DAYS TO HEADING 8 / Protein HEADING DATE 5 / Transcriptional activator HAP3H / OsHAP3H / OsGhd8


Mass: 10092.552 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: OsGhd8 / Source: (gene. exp.) Oryza sativa (Asian cultivated rice)
Gene: HD5, DTH8, GHD8, HAP3H, NFYB11, Os08g0174500, LOC_Os08g07740
Production host: Escherichia coli (E. coli) / References: UniProt: Q0J7P4
#2: Protein OsNF-YC7 / OsNF-YC7


Mass: 8806.335 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: OsNF-YC7 / Source: (gene. exp.) Oryza sativa (Asian cultivated rice) / Gene: Os09g0480700, OSNPB_090480700 / Production host: Escherichia coli (E. coli) / References: UniProt: Q0J0W2, UniProt: Q9XE33*PLUS
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.98 Å3/Da / Density % sol: 37.99 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 20% PEG 4000, 0.1 M sodium acetate pH 5.0, 0.2 M ammonium acetate

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9677 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.7→45.21 Å / Num. obs: 38743 / % possible obs: 99.6 % / Observed criterion σ(I): 2.1 / Redundancy: 6.9 % / Biso Wilson estimate: 13.03 Å2 / CC1/2: 0.967 / Net I/σ(I): 3.6
Reflection shellResolution: 1.7→1.76 Å / Mean I/σ(I) obs: 2.1 / Num. unique obs: 3887 / CC1/2: 0.596 / Rpim(I) all: 0.356 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5G49

5g49


Resolution: 2.7→44.77 Å / Cor.coef. Fo:Fc: 0.838 / Cor.coef. Fo:Fc free: 0.819 / SU B: 18.561 / SU ML: 0.383 / Cross valid method: THROUGHOUT / ESU R Free: 0.451 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27638 224 5.4 %RANDOM
Rwork0.2575 ---
obs0.25851 3947 98.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.906 Å2
Baniso -1Baniso -2Baniso -3
1--2.14 Å20 Å2-1.74 Å2
2---3.15 Å20 Å2
3---5.52 Å2
Refinement stepCycle: 1 / Resolution: 2.7→44.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1322 0 12 41 1375
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0131353
X-RAY DIFFRACTIONr_bond_other_d0.0020.0171329
X-RAY DIFFRACTIONr_angle_refined_deg1.1411.6511814
X-RAY DIFFRACTIONr_angle_other_deg1.4081.5853065
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5155163
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.63420.2677
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.23815256
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.9271515
X-RAY DIFFRACTIONr_chiral_restr0.0570.2180
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021476
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02301
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2421.885658
X-RAY DIFFRACTIONr_mcbond_other1.2391.88657
X-RAY DIFFRACTIONr_mcangle_it2.1742.812819
X-RAY DIFFRACTIONr_mcangle_other2.1742.818820
X-RAY DIFFRACTIONr_scbond_it1.0222.072694
X-RAY DIFFRACTIONr_scbond_other1.0222.075695
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.4293.049995
X-RAY DIFFRACTIONr_long_range_B_refined6.82132.7635169
X-RAY DIFFRACTIONr_long_range_B_other6.82132.7685170
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.701→2.771 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 22 -
Rwork0.309 286 -
obs--100 %

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