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- PDB-6xzn: Arabidopsis UV-B photoreceptor UVR8 mutant G101S W285A -

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Basic information

Entry
Database: PDB / ID: 6xzn
TitleArabidopsis UV-B photoreceptor UVR8 mutant G101S W285A
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
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Ultraviolet-B receptor UVR8
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ultraviolet-B receptor UVR8
B: Ultraviolet-B receptor UVR8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,9947
Polymers80,4042
Non-polymers5915
Water4,252236
1
A: Ultraviolet-B receptor UVR8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4003
Polymers40,2021
Non-polymers1982
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ultraviolet-B receptor UVR8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5944
Polymers40,2021
Non-polymers3923
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.541, 99.123, 132.727
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2

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Components

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


Mass: 40201.832 Da / Num. of mol.: 2 / Mutation: G101S W285A
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.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 236 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.07 Å3/Da / Density % sol: 40.51 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 0.2M Sodium nitrate 0.1M Bis Tris propane pH 8.5 20% w/v PEG 3350. 20% 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: Nov 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→40.4 Å / Num. obs: 67187 / % possible obs: 98.68 % / Redundancy: 13.4 % / Biso Wilson estimate: 28.8 Å2 / CC1/2: 1 / Net I/σ(I): 21.71
Reflection shellResolution: 1.751→1.813 Å / Num. unique obs: 6556 / CC1/2: 0.659

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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: 1.75→40.4 Å / SU ML: 0.2008 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.8706
RfactorNum. reflection% reflection
Rfree0.2206 3316 4.94 %
Rwork0.1552 --
obs0.1585 67142 98.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 40.99 Å2
Refinement stepCycle: LAST / Resolution: 1.75→40.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5534 0 39 236 5809
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00975786
X-RAY DIFFRACTIONf_angle_d1.05667840
X-RAY DIFFRACTIONf_chiral_restr0.0625824
X-RAY DIFFRACTIONf_plane_restr0.00611028
X-RAY DIFFRACTIONf_dihedral_angle_d23.0085832
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.780.39911390.29712554X-RAY DIFFRACTION96.32
1.78-1.80.32941490.27562596X-RAY DIFFRACTION97.65
1.8-1.830.30551200.24692600X-RAY DIFFRACTION98.02
1.83-1.860.29731370.23762624X-RAY DIFFRACTION97.94
1.86-1.890.32051430.22592572X-RAY DIFFRACTION98.09
1.89-1.930.30311350.20712624X-RAY DIFFRACTION98.25
1.93-1.960.28541270.19642619X-RAY DIFFRACTION98.35
1.96-20.27091370.17752607X-RAY DIFFRACTION98.39
2-2.050.24171440.16262618X-RAY DIFFRACTION98.54
2.05-2.10.22051310.15282659X-RAY DIFFRACTION98.41
2.1-2.150.23881030.14792653X-RAY DIFFRACTION98.46
2.15-2.210.22771310.14372661X-RAY DIFFRACTION98.62
2.21-2.270.22491470.15052627X-RAY DIFFRACTION98.93
2.27-2.340.22451480.14392623X-RAY DIFFRACTION99.14
2.34-2.430.23871450.15872649X-RAY DIFFRACTION98.73
2.43-2.520.27081330.16192714X-RAY DIFFRACTION99.34
2.52-2.640.23511370.15592639X-RAY DIFFRACTION98.97
2.64-2.780.21631240.16382699X-RAY DIFFRACTION99.19
2.78-2.950.27041290.16292699X-RAY DIFFRACTION99.4
2.95-3.180.23351550.16632692X-RAY DIFFRACTION99.55
3.18-3.50.20431490.14372686X-RAY DIFFRACTION99.44
3.5-4.010.21561490.12922727X-RAY DIFFRACTION99.58
4.01-5.050.14951580.12112771X-RAY DIFFRACTION99.59
5.05-40.40.20681460.1632913X-RAY DIFFRACTION99.58

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