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- PDB-4d9s: Crystal structure of Arabidopsis thaliana UVR8 (UV Resistance locus 8) -

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Basic information

Entry
Database: PDB / ID: 4d9s
TitleCrystal structure of Arabidopsis thaliana UVR8 (UV Resistance locus 8)
ComponentsUVB-resistance protein UVR8
Keywordschromatin-binding protein / UV resistance / UV-B photoreceptor / tryptophan chromophores / homodimer / 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: 1.701 Å
AuthorsArvai, A.S. / Christie, J.M. / Pratt, A.J. / Hitomi, K. / Getzoff, E.D.
CitationJournal: Science / Year: 2012
Title: Plant UVR8 Photoreceptor Senses UV-B by Tryptophan-Mediated Disruption of Cross-Dimer Salt Bridges.
Authors: Christie, J.M. / Arvai, A.S. / Baxter, K.J. / Heilmann, M. / Pratt, A.J. / O'Hara, A. / Kelly, S.M. / Hothorn, M. / Smith, B.O. / Hitomi, K. / Jenkins, G.I. / Getzoff, E.D.
History
DepositionJan 11, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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: UVB-resistance protein UVR8
B: UVB-resistance protein UVR8


Theoretical massNumber of molelcules
Total (without water)87,1022
Polymers87,1022
Non-polymers00
Water15,889882
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: UVB-resistance protein UVR8


Theoretical massNumber of molelcules
Total (without water)43,5511
Polymers43,5511
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: UVB-resistance protein UVR8


Theoretical massNumber of molelcules
Total (without water)43,5511
Polymers43,5511
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.117, 51.511, 97.084
Angle α, β, γ (deg.)90.00, 102.89, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe asymmetric unit is the biological unit

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Components

#1: Protein UVB-resistance protein UVR8 / AT5g63860/MGI19_6U / At5g63860/MGI19_6 / Protein UV-B resistance 8


Mass: 43551.238 Da / Num. of mol.: 2 / Fragment: UNP residues 1-405
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: UVR8, At5g63860, AT5G63860 / Plasmid: pMH-HSsumo / Production host: Escherichia coli (E. coli) / References: UniProt: Q9FN03
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 882 / 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: 1.91 Å3/Da / Density % sol: 35.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6
Details: MPEG 2K, NACL, pH 6.0, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97945 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 9, 2011
RadiationMonochromator: synchrotron / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 72086 / Num. obs: 73086 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.7→1.76 Å / % possible all: 97.4

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.2_869)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KCI

3kci


Resolution: 1.701→49.421 Å / SU ML: 0.4 / σ(F): 0 / Phase error: 19.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1939 1874 2.77 %RANDOM
Rwork0.1596 ---
obs0.1605 67573 93.38 %-
all-72086 --
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 33.819 Å2 / ksol: 0.355 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.9562 Å20 Å26.3734 Å2
2---6.2171 Å20 Å2
3---9.1733 Å2
Refinement stepCycle: LAST / Resolution: 1.701→49.421 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5779 0 0 882 6661
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055915
X-RAY DIFFRACTIONf_angle_d0.9868019
X-RAY DIFFRACTIONf_dihedral_angle_d13.8532076
X-RAY DIFFRACTIONf_chiral_restr0.075844
X-RAY DIFFRACTIONf_plane_restr0.0041054
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7012-1.74720.34131210.25994249X-RAY DIFFRACTION79
1.7472-1.79860.2851300.23054516X-RAY DIFFRACTION84
1.7986-1.85670.31231330.2144699X-RAY DIFFRACTION87
1.8567-1.9230.22851370.18714794X-RAY DIFFRACTION89
1.923-20.21451450.17284984X-RAY DIFFRACTION93
2-2.0910.19151420.16585130X-RAY DIFFRACTION95
2.091-2.20130.19211520.15585212X-RAY DIFFRACTION96
2.2013-2.33920.20261460.15015226X-RAY DIFFRACTION96
2.3392-2.51980.19871500.1575216X-RAY DIFFRACTION97
2.5198-2.77340.1751490.15765286X-RAY DIFFRACTION98
2.7734-3.17460.21451540.15855355X-RAY DIFFRACTION99
3.1746-3.99940.14551550.13075459X-RAY DIFFRACTION100
3.9994-49.44140.15811600.14045573X-RAY DIFFRACTION100

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