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- PDB-4dnu: Crystal structure of the W285A mutant of UVB-resistance protein UVR8 -

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Basic information

Entry
Database: PDB / ID: 4dnu
TitleCrystal structure of the W285A 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 / 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 / SAD / Resolution: 1.764 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AT5g63860/MGI19_6


Theoretical massNumber of molelcules
Total (without water)40,2421
Polymers40,2421
Non-polymers00
Water7,963442
1
A: AT5g63860/MGI19_6

A: AT5g63860/MGI19_6


Theoretical massNumber of molelcules
Total (without water)80,4842
Polymers80,4842
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.159, 107.981, 111.846
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-410-

HOH

21A-541-

HOH

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Components

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


Mass: 40241.840 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 10-381 / Mutation: W285A
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.: 442 / 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: 2.48 Å3/Da / Density % sol: 50.44 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 23%(w/v) PEG 3350, 100mM Bis-Tris pH6.0, 3%(w/v) 1,5-diaminopentane dihydrochloride, 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: 1.76→50 Å / Num. all: 76697 / Num. obs: 75086 / % possible obs: 97.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 1.76→1.82 Å / % possible all: 90.6

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Processing

Software
NameVersionClassification
CBASSdata collection
SHELXSphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.764→32.48 Å / SU ML: 0.32 / σ(F): 0.88 / Phase error: 16.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1685 3795 5.06 %RANDOM
Rwork0.152 ---
all0.1529 76697 --
obs0.1529 75068 98.5 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.257 Å2 / ksol: 0.379 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--5.2547 Å2-0 Å20 Å2
2---5.6202 Å2-0 Å2
3---10.8401 Å2
Refinement stepCycle: LAST / Resolution: 1.764→32.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2810 0 0 442 3252
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132897
X-RAY DIFFRACTIONf_angle_d1.2263934
X-RAY DIFFRACTIONf_dihedral_angle_d13.8161020
X-RAY DIFFRACTIONf_chiral_restr0.092416
X-RAY DIFFRACTIONf_plane_restr0.005519
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7642-1.78650.22641220.2019247593
1.7865-1.810.2421400.19792663100
1.81-1.83480.21981530.18692706100
1.8348-1.8610.22091270.18452638100
1.861-1.88880.20441370.16852705100
1.8888-1.91830.17911180.16082717100
1.9183-1.94980.20511200.1584265699
1.9498-1.98340.13461590.14662639100
1.9834-2.01940.20111540.1384266699
2.0194-2.05830.15851480.1402266599
2.0583-2.10030.15791330.1427266699
2.1003-2.14590.1291520.1394262299
2.1459-2.19580.18431430.141265599
2.1958-2.25070.14831400.1441268599
2.2507-2.31160.16721360.1472263999
2.3116-2.37960.1961610.1543266299
2.3796-2.45640.18621370.1486265699
2.4564-2.54410.14861230.1514269499
2.5441-2.64590.16411390.152268699
2.6459-2.76630.16621740.1565259199
2.7663-2.91210.18861550.15265599
2.9121-3.09440.18281410.1577263598
3.0944-3.33310.16431460.1461252795
3.3331-3.66810.16741490.1371253295
3.6681-4.19790.1261220.1277256495
4.1979-5.28520.13911580.1391259698
5.2852-32.48540.17891080.1984267899
Refinement TLS params.Method: refined / Origin x: -21.4021 Å / Origin y: -12.001 Å / Origin z: 28.8098 Å
111213212223313233
T0.0525 Å20.0053 Å2-0.0032 Å2-0.0458 Å2-0.0058 Å2--0.0548 Å2
L0.2226 °2-0.0014 °2-0.0168 °2-0.1255 °2-0.0694 °2--0.106 °2
S-0.0034 Å °0.0116 Å °-0.074 Å °0.0183 Å °0.0111 Å °-0.0392 Å °0.0226 Å °0.0146 Å °0.1938 Å °
Refinement TLS groupSelection details: ALL

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