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- PDB-4dnv: Crystal structure of the W285F mutant of UVB-resistance protein UVR8 -

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Basic information

Entry
Database: PDB / ID: 4dnv
TitleCrystal structure of the W285F mutant 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 / 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 / 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: 1.999 Å
AuthorsWu, D. / Hu, Q. / Yan, Z. / Chen, W. / Yan, C. / Zhang, J. / 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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
C: AT5g63860/MGI19_6
D: AT5g63860/MGI19_6


Theoretical massNumber of molelcules
Total (without water)159,3454
Polymers159,3454
Non-polymers00
Water11,854658
1
A: AT5g63860/MGI19_6
B: AT5g63860/MGI19_6


Theoretical massNumber of molelcules
Total (without water)79,6732
Polymers79,6732
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: AT5g63860/MGI19_6
D: AT5g63860/MGI19_6


Theoretical massNumber of molelcules
Total (without water)79,6732
Polymers79,6732
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: AT5g63860/MGI19_6


Theoretical massNumber of molelcules
Total (without water)39,8361
Polymers39,8361
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
B: AT5g63860/MGI19_6


Theoretical massNumber of molelcules
Total (without water)39,8361
Polymers39,8361
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
C: AT5g63860/MGI19_6


Theoretical massNumber of molelcules
Total (without water)39,8361
Polymers39,8361
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
D: AT5g63860/MGI19_6


Theoretical massNumber of molelcules
Total (without water)39,8361
Polymers39,8361
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.571, 67.214, 93.626
Angle α, β, γ (deg.)85.06, 81.45, 66.04
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 39836.332 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 12-381 / Mutation: W285F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At5g63860, UVR8 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9FN03
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 658 / 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: 1.98 Å3/Da / Density % sol: 37.95 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 17%(w/v) PEG 8000, 100mM Tris pH8.5, 200mM Magnesium Chloride, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 10, 2011
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.999→40 Å / Num. all: 82487 / Num. obs: 77456 / % possible obs: 93.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 1.999→2.07 Å / % possible all: 94.9

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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: 1.999→33.016 Å / SU ML: 0.48 / σ(F): 1.96 / Phase error: 27.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2399 3874 5 %RANDOM
Rwork0.2067 ---
all0.2084 82487 --
obs0.2084 77434 93.5 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 30.48 Å2 / ksol: 0.318 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-8.121 Å21.6552 Å2-7.0753 Å2
2---11.4455 Å2-2.2996 Å2
3---3.8766 Å2
Refinement stepCycle: LAST / Resolution: 1.999→33.016 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11180 0 0 658 11838
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00811459
X-RAY DIFFRACTIONf_angle_d1.08215533
X-RAY DIFFRACTIONf_dihedral_angle_d16.6524031
X-RAY DIFFRACTIONf_chiral_restr0.0781633
X-RAY DIFFRACTIONf_plane_restr0.0062042
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 28

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.999-2.02340.35691140.2904243286
2.0234-2.0490.26791360.2606268995
2.049-2.0760.33121500.2615263495
2.076-2.10440.27471550.249268595
2.1044-2.13450.33811180.2452266295
2.1345-2.16630.25661500.2509267495
2.1663-2.20020.2741330.2496263796
2.2002-2.23620.28851520.2467270196
2.2362-2.27480.26321430.249265395
2.2748-2.31620.32881330.237276295
2.3162-2.36070.29481380.2506262495
2.3607-2.40890.29131600.2498272095
2.4089-2.46120.29811370.2455262596
2.4612-2.51850.28561440.2456270095
2.5185-2.58140.27781320.2417267795
2.5814-2.65120.29021340.2356269796
2.6512-2.72920.31641340.2337264195
2.7292-2.81720.25741340.2351269495
2.8172-2.91780.26411260.2344265894
2.9178-3.03460.25021610.2175256994
3.0346-3.17260.24791420.2107257292
3.1726-3.33970.23031230.1865260392
3.3397-3.54870.1911330.1711255591
3.5487-3.82230.18341420.1652243888
3.8223-4.20630.18071350.1501252689
4.2063-4.81340.18521420.1602240087
4.8134-6.05820.1771250.1708268095
6.0582-33.020.23751480.1949265294
Refinement TLS params.Method: refined / Origin x: 26.2165 Å / Origin y: 6.1229 Å / Origin z: 57.6135 Å
111213212223313233
T0.1122 Å20.002 Å20.0036 Å2-0.1475 Å2-0.0114 Å2--0.1874 Å2
L0.1028 °2-0.0242 °20.0905 °2-0.1423 °2-0.0933 °2--0.7995 °2
S0.0132 Å °0.0128 Å °0.022 Å °0.0291 Å °0.0393 Å °-0.0907 Å °0.0202 Å °0.0486 Å °-0.0451 Å °
Refinement TLS groupSelection details: ALL

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