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- PDB-6xzl: Arabidopsis UV-B photoreceptor UVR8 mutant D96N D107N -

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Basic information

Entry
Database: PDB / ID: 6xzl
TitleArabidopsis UV-B photoreceptor UVR8 mutant D96N D107N
ComponentsUltraviolet-B receptor UVR8
KeywordsPLANT PROTEIN / UVB / photoreceptor
Function / homology
Function and homology information


entrainment of circadian clock / response to UV-B / plastid / photoreceptor activity / response to UV / guanyl-nucleotide exchange factor activity / chromatin binding / chromatin / protein homodimerization activity / identical protein binding ...entrainment of circadian clock / response to UV-B / plastid / photoreceptor activity / response to UV / guanyl-nucleotide exchange factor activity / chromatin binding / chromatin / protein homodimerization activity / identical protein binding / nucleus / cytosol
Similarity search - Function
Regulator of chromosome condensation (RCC1) signature 2. / Regulator of chromosome condensation (RCC1) repeat / Regulator of chromosome condensation, RCC1 / Regulator of chromosome condensation (RCC1) repeat profile. / Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II
Similarity search - Domain/homology
Ultraviolet-B receptor UVR8
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.39 Å
AuthorsLau, K. / Hothorn, M.
Funding support Switzerland, 2items
OrganizationGrant numberCountry
Swiss National Science Foundation31003A_175774 Switzerland
European Research Council (ERC)310539 Switzerland
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2021
Title: A constitutively monomeric UVR8 photoreceptor confers enhanced UV-B photomorphogenesis.
Authors: Podolec, R. / Lau, K. / Wagnon, T.B. / Hothorn, M. / Ulm, R.
History
DepositionFeb 4, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 13, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 28, 2021Group: 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.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 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

Downloads & links

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Assembly

Deposited unit
A: Ultraviolet-B receptor UVR8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4132
Polymers40,3211
Non-polymers921
Water4,161231
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint-1 kcal/mol
Surface area13750 Å2
Unit cell
Length a, b, c (Å)97.614, 50.980, 70.488
Angle α, β, γ (deg.)90.000, 104.948, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein Ultraviolet-B receptor UVR8 / Protein UV-B RESISTANCE 8 / RCC1 domain-containing protein UVR8


Mass: 40321.043 Da / Num. of mol.: 1 / Mutation: D96N D107N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: UVR8, At5g63860, MGI19.7 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9FN03
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 231 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.1 Å3/Da / Density % sol: 41.46 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: Methylated protein. 0.1M TRIS 8.5, 0.1M NaCl, 30% PEG4000, 1.8mg/mL, 2:1, prot:buffer. 25% glycerol cryoprotectant

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Dec 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.39→47.16 Å / Num. obs: 67424 / % possible obs: 99.97 % / Redundancy: 6.6 % / Biso Wilson estimate: 17.05 Å2 / CC1/2: 0.996 / Net I/σ(I): 8.97
Reflection shellResolution: 1.39→1.44 Å / Num. unique obs: 6711 / CC1/2: 0.599

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4D9S

4d9s


Resolution: 1.39→47.16 Å / SU ML: 0.1411 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.4821
RfactorNum. reflection% reflection
Rfree0.1793 3470 5.15 %
Rwork0.1439 --
obs0.1458 67411 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 23.4 Å2
Refinement stepCycle: LAST / Resolution: 1.39→47.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2816 0 6 231 3053
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00982940
X-RAY DIFFRACTIONf_angle_d1.02794002
X-RAY DIFFRACTIONf_chiral_restr0.0848420
X-RAY DIFFRACTIONf_plane_restr0.0056522
X-RAY DIFFRACTIONf_dihedral_angle_d21.8125452
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.39-1.410.32141460.292538X-RAY DIFFRACTION99.85
1.41-1.430.33061240.25642524X-RAY DIFFRACTION99.96
1.43-1.450.29491370.25532580X-RAY DIFFRACTION100
1.45-1.470.27421510.23052506X-RAY DIFFRACTION100
1.47-1.50.29621430.21582563X-RAY DIFFRACTION100
1.5-1.520.23741340.19372535X-RAY DIFFRACTION100
1.52-1.550.23781400.17362551X-RAY DIFFRACTION100
1.55-1.580.22891530.16522525X-RAY DIFFRACTION99.96
1.58-1.610.19611460.16012539X-RAY DIFFRACTION100
1.61-1.650.21191270.14892565X-RAY DIFFRACTION100
1.65-1.690.21621480.13982514X-RAY DIFFRACTION99.92
1.69-1.730.16711410.12622544X-RAY DIFFRACTION100
1.73-1.780.16581370.11612589X-RAY DIFFRACTION100
1.78-1.830.17861400.12492521X-RAY DIFFRACTION99.89
1.83-1.890.19791390.1272549X-RAY DIFFRACTION99.93
1.89-1.950.15831300.12122563X-RAY DIFFRACTION100
1.95-2.030.18991310.12042575X-RAY DIFFRACTION100
2.03-2.120.14971450.11682551X-RAY DIFFRACTION99.96
2.12-2.240.14971140.11952578X-RAY DIFFRACTION100
2.24-2.380.16461180.12432580X-RAY DIFFRACTION99.96
2.38-2.560.18711510.13472550X-RAY DIFFRACTION100
2.56-2.820.17011350.14482589X-RAY DIFFRACTION100
2.82-3.230.18581460.14762581X-RAY DIFFRACTION99.89
3.23-4.060.14831440.1322567X-RAY DIFFRACTION99.93
4.06-47.160.16661500.15672664X-RAY DIFFRACTION99.93

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