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- PDB-4dnw: Crystal structure of UVB-resistance protein UVR8 -

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Basic information

Entry
Database: PDB / ID: 4dnw
TitleCrystal structure of UVB-resistance protein UVR8
ComponentsAT5g63860/MGI19_6
KeywordsGENE REGULATION / WD40 Repeats / UV-B perception / COP1
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 1/beta-lactamase-inhibitor protein II / 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 / 7 Propeller / Methylamine Dehydrogenase; Chain H / Mainly Beta
Similarity search - Domain/homology
Ultraviolet-B receptor UVR8
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.773 Å
AuthorsWu, D. / Hu, Q. / Yan, Z. / Chen, W. / Yan, C. / Wang, J. / Shi, Y.
CitationJournal: Nature / Year: 2012
Title: Structural basis of ultraviolet-B perception by UVR8.
Authors: Wu, D. / Hu, Q. / Yan, Z. / Chen, W. / Yan, C. / Huang, X. / Zhang, J. / Yang, P. / Deng, H. / Wang, J. / Deng, X. / Shi, Y.
History
DepositionFeb 9, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 7, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2012Group: Database references
Revision 1.2Jul 17, 2013Group: Database references
Revision 1.3Nov 8, 2023Group: 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: AT5g63860/MGI19_6
B: AT5g63860/MGI19_6


Theoretical massNumber of molelcules
Total (without water)80,4372
Polymers80,4372
Non-polymers00
Water10,233568
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: AT5g63860/MGI19_6


Theoretical massNumber of molelcules
Total (without water)40,2191
Polymers40,2191
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: AT5g63860/MGI19_6


Theoretical massNumber of molelcules
Total (without water)40,2191
Polymers40,2191
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)120.646, 61.517, 103.167
Angle α, β, γ (deg.)90.00, 118.00, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein AT5g63860/MGI19_6 / Protein UV-B resistance 8 / UVB-resistance protein UVR8


Mass: 40218.711 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 12-385
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: UVR8, At5g63860, AT5G63860 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9FN03
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 568 / Source method: isolated from a natural source / Formula: H2O

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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: 291 K / Method: vapor diffusion, hanging drop / pH: 9.2
Details: 18%(w/v) PEG 8000, 100mM Tris pH9.2, 200mM Magnesium Chloride, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1.07214 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Oct 10, 2011
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07214 Å / Relative weight: 1
ReflectionResolution: 1.77→50 Å / Num. all: 64723 / Num. obs: 63040 / % possible obs: 97.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 1.77→1.83 Å / % possible all: 92

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DNU

4dnu


Resolution: 1.773→32.294 Å / SU ML: 0.41 / σ(F): 1.33 / Phase error: 20.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2012 3192 5.07 %RANDOM
Rwork0.171 ---
all0.1726 64723 --
obs0.1726 63012 97.11 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.399 Å2 / ksol: 0.425 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--5.267 Å20 Å20.8625 Å2
2--4.9209 Å20 Å2
3----2.323 Å2
Refinement stepCycle: LAST / Resolution: 1.773→32.294 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5629 0 0 568 6197
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075836
X-RAY DIFFRACTIONf_angle_d0.9657926
X-RAY DIFFRACTIONf_dihedral_angle_d15.9022059
X-RAY DIFFRACTIONf_chiral_restr0.073830
X-RAY DIFFRACTIONf_plane_restr0.0051046
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7731-1.79960.29761070.2635226084
1.7996-1.82770.26081480.2506247393
1.8277-1.85760.26261270.2292252596
1.8576-1.88970.27281190.2125256596
1.8897-1.9240.23821220.1972258597
1.924-1.9610.21671520.1833257097
1.961-2.0010.22631370.1764260997
2.001-2.04460.22281560.1692258898
2.0446-2.09210.21331340.1692257797
2.0921-2.14440.22251390.176259998
2.1444-2.20240.18791460.1699263498
2.2024-2.26720.23121240.1716261798
2.2672-2.34030.20881510.1719258097
2.3403-2.42390.20931450.1746263398
2.4239-2.5210.21981370.1762260798
2.521-2.63560.21151290.1758265499
2.6356-2.77450.2131460.1827265199
2.7745-2.94830.19541490.1813265399
2.9483-3.17570.20461330.1828263299
3.1757-3.4950.18581530.1536264999
3.495-3.99990.15241480.1357270199
3.9999-5.03630.14011290.1296270099
5.0363-32.2990.20451610.1824275899
Refinement TLS params.Method: refined / Origin x: 29.1946 Å / Origin y: -19.727 Å / Origin z: 23.4131 Å
111213212223313233
T0.0813 Å20.0332 Å2-0.002 Å2-0.0923 Å20.0213 Å2--0.0532 Å2
L0.5631 °20.0492 °2-0.0347 °2-0.2056 °20.0443 °2--0.2207 °2
S-0.0462 Å °-0.3477 Å °-0.0108 Å °0.0245 Å °0.0438 Å °0.0193 Å °0.0147 Å °0.0248 Å °-0.0447 Å °
Refinement TLS groupSelection details: all

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