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- PDB-6xzm: Arabidopsis UV-B photoreceptor UVR8 mutant D96N D107N W285A -

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Basic information

Entry
Database: PDB / ID: 6xzm
TitleArabidopsis UV-B photoreceptor UVR8 mutant D96N D107N 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
: / RCC1-like domain / Regulator of chromosome condensation (RCC1) repeat / Regulator of chromosome condensation (RCC1) signature 2. / 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
NITRATE ION / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Ultraviolet-B receptor UVR8
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.10009315021 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 9, 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)80,90410
Polymers80,1872
Non-polymers7178
Water1,35175
1
A: Ultraviolet-B receptor UVR8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3244
Polymers40,0941
Non-polymers2303
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ultraviolet-B receptor UVR8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5806
Polymers40,0941
Non-polymers4865
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.266, 98.266, 138.836
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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Components

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


Mass: 40093.723 Da / Num. of mol.: 2 / Mutation: D96N D107N 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-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: NO3
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 2.41 Å3/Da / Density % sol: 49.03 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 22% PEG3350, 0.2M NaNO3, 5mg/mL. 20% PEG400 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: Aug 31, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→49.13 Å / Num. obs: 45831 / % possible obs: 99.95 % / Redundancy: 20.1 % / Biso Wilson estimate: 42.1418773177 Å2 / CC1/2: 0.999 / Net I/σ(I): 13.84
Reflection shellResolution: 2.1→2.175 Å / Num. unique obs: 4521 / CC1/2: 0.483

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4D9S

4d9s


Resolution: 2.10009315021→49.13 Å / SU ML: 0.289283250111 / Cross valid method: FREE R-VALUE / σ(F): 1.33648739498 / Phase error: 30.6166883102
RfactorNum. reflection% reflection
Rfree0.248131330672 2200 4.80192076831 %
Rwork0.197002582858 --
obs0.199549219029 45815 99.9650891318 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 53.3098685346 Å2
Refinement stepCycle: LAST / Resolution: 2.10009315021→49.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5492 0 47 75 5614
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01110078115955667
X-RAY DIFFRACTIONf_angle_d1.140695702137677
X-RAY DIFFRACTIONf_chiral_restr0.0636319687915814
X-RAY DIFFRACTIONf_plane_restr0.007121874003251008
X-RAY DIFFRACTIONf_dihedral_angle_d14.73911302943216
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1001-2.14580.3895131481651290.3463467622832684X-RAY DIFFRACTION99.9644633973
2.1458-2.19570.3488687923211460.3189839123522666X-RAY DIFFRACTION99.9644507643
2.1957-2.25060.3410332527651330.2893775161892710X-RAY DIFFRACTION100
2.2506-2.31140.3571061706721590.2753156864992646X-RAY DIFFRACTION99.9643620813
2.3114-2.37940.2564203980591020.2624146956152754X-RAY DIFFRACTION99.9649982499
2.3794-2.45620.3336666856611440.2440762548392701X-RAY DIFFRACTION99.8595998596
2.4562-2.5440.3001557970491440.2261418918912673X-RAY DIFFRACTION100
2.544-2.64590.3002657542211260.2246067833642733X-RAY DIFFRACTION99.965034965
2.6459-2.76630.288783890811190.2242346668192686X-RAY DIFFRACTION100
2.7663-2.91210.3023135924231340.2274252542392723X-RAY DIFFRACTION100
2.9121-3.09450.302367295441460.2282112463322752X-RAY DIFFRACTION100
3.0945-3.33340.231278573241330.2235876754252716X-RAY DIFFRACTION99.9649122807
3.3334-3.66880.2599327315941480.1914778997912723X-RAY DIFFRACTION100
3.6688-4.19940.2055168898251460.1526849446652742X-RAY DIFFRACTION100
4.1994-5.28980.1718439627311210.1405108367252826X-RAY DIFFRACTION100
5.2898-49.130.22107295861700.1719714517172880X-RAY DIFFRACTION99.8363338789

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