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- PDB-6dd7: Crystal structure of plant UVB photoreceptor UVR8 from in situ se... -

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Basic information

Entry
Database: PDB / ID: 6dd7
TitleCrystal structure of plant UVB photoreceptor UVR8 from in situ serial Laue diffraction
ComponentsUltraviolet-B receptor UVR8
KeywordsGENE REGULATION / photoreceptor / Laue diffraction / serial crystallography / in situ diffraction
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 / FOURIER SYNTHESIS / Resolution: 2 Å
AuthorsRen, Z.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Eye Institute (NIH/NEI)R01EY024363 United States
CitationJournal: Lab Chip / Year: 2018
Title: Crystal-on-crystal chips for in situ serial diffraction at room temperature.
Authors: Ren, Z. / Ayhan, M. / Bandara, S. / Bowatte, K. / Kumarapperuma, I. / Gunawardana, S. / Shin, H. / Wang, C. / Zeng, X. / Yang, X.
History
DepositionMay 9, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 18, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 8, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 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: Ultraviolet-B receptor UVR8
B: Ultraviolet-B receptor UVR8
C: Ultraviolet-B receptor UVR8
D: Ultraviolet-B receptor UVR8


Theoretical massNumber of molelcules
Total (without water)163,5024
Polymers163,5024
Non-polymers00
Water17,799988
1
A: Ultraviolet-B receptor UVR8
D: Ultraviolet-B receptor UVR8


Theoretical massNumber of molelcules
Total (without water)81,7512
Polymers81,7512
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ultraviolet-B receptor UVR8
C: Ultraviolet-B receptor UVR8


Theoretical massNumber of molelcules
Total (without water)81,7512
Polymers81,7512
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)111.200, 80.300, 190.000
Angle α, β, γ (deg.)90.00, 94.80, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-667-

HOH

21C-650-

HOH

31D-591-

HOH

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Components

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


Mass: 40875.438 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: UVR8, At5g63860, MGI19.7 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9FN03
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 988 / 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: 2.59 Å3/Da / Density % sol: 52.42 %
Crystal growTemperature: 294 K / Method: microbatch / pH: 9.2
Details: 3.5 mg/mL protein, 7-10% PEG 8000, 50 mM MgCl2, and 50 mM tris buffer at pH 9.2

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Data collection

DiffractionMean temperature: 294 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 1-1.25
DetectorType: RAYONIX MX340-HS / Detector: CCD / Date: Aug 24, 2015 / Details: KB mirrors
RadiationProtocol: LAUE / Monochromatic (M) / Laue (L): L / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.251
ReflectionResolution: 2→100 Å / Num. obs: 99141 / % possible obs: 85.9 % / Redundancy: 7.6 % / Net I/σ(I): 10.3
Reflection shellResolution: 2→2.1 Å

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
Precognitiondata reduction
Epinormdata reduction
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4naa

4naa


Resolution: 2→47.333 Å / SU ML: 0.56 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 43.08
RfactorNum. reflection% reflection
Rfree0.3281 4938 5.06 %
Rwork0.2535 --
obs0.2574 97644 86.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→47.333 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11172 0 0 988 12160
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00911440
X-RAY DIFFRACTIONf_angle_d1.05415508
X-RAY DIFFRACTIONf_dihedral_angle_d16.2456528
X-RAY DIFFRACTIONf_chiral_restr0.0591628
X-RAY DIFFRACTIONf_plane_restr0.0062032
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.02270.464540.3462847X-RAY DIFFRACTION24
2.0227-2.04650.3689490.37021296X-RAY DIFFRACTION37
2.0465-2.07150.41811000.36861723X-RAY DIFFRACTION48
2.0715-2.09770.37711030.35332140X-RAY DIFFRACTION60
2.0977-2.12530.41831280.32852511X-RAY DIFFRACTION70
2.1253-2.15440.39881570.32352674X-RAY DIFFRACTION77
2.1544-2.18520.38671480.34362944X-RAY DIFFRACTION83
2.1852-2.21780.3651650.36133143X-RAY DIFFRACTION87
2.2178-2.25250.37881500.37273171X-RAY DIFFRACTION90
2.2525-2.28940.43231970.36633281X-RAY DIFFRACTION91
2.2894-2.32890.42021740.36333291X-RAY DIFFRACTION94
2.3289-2.37120.42061690.35523443X-RAY DIFFRACTION95
2.3712-2.41680.38782000.33763366X-RAY DIFFRACTION96
2.4168-2.46620.41142010.32613412X-RAY DIFFRACTION97
2.4662-2.51980.39211820.31453439X-RAY DIFFRACTION97
2.5198-2.57840.36021800.31363456X-RAY DIFFRACTION97
2.5784-2.64290.37181780.30383505X-RAY DIFFRACTION97
2.6429-2.71430.3891820.30543460X-RAY DIFFRACTION98
2.7143-2.79420.3751690.29393462X-RAY DIFFRACTION98
2.7942-2.88440.37961730.29093549X-RAY DIFFRACTION98
2.8844-2.98750.3531850.2813490X-RAY DIFFRACTION97
2.9875-3.1070.36441950.25283437X-RAY DIFFRACTION97
3.107-3.24840.33411920.22693443X-RAY DIFFRACTION97
3.2484-3.41960.30911980.20553455X-RAY DIFFRACTION97
3.4196-3.63380.27081820.17763476X-RAY DIFFRACTION97
3.6338-3.91430.27461880.16523444X-RAY DIFFRACTION97
3.9143-4.30790.22871890.15393517X-RAY DIFFRACTION97
4.3079-4.93070.22511760.15233529X-RAY DIFFRACTION98
4.9307-6.210.24711810.15753531X-RAY DIFFRACTION97
6.21-47.34660.24191930.17993271X-RAY DIFFRACTION89
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.4226-0.5071-0.56811.4531-0.66781.25160.1493-0.13880.3826-0.0592-0.0477-0.1742-0.12030.1111-0.09710.324-0.09740.04620.7432-0.09490.5117130.1382-12.628921.9048
21.6907-0.4102-0.35510.9641-0.39961.43530.04570.18410.186-0.1326-0.04090.0476-0.2723-0.23590.00760.22240.0665-0.02540.21230.02030.191284.0915-10.020572.9272
31.40150.1238-0.07160.87630.06811.16230.04950.1015-0.1104-0.1666-0.0385-0.1861-0.02140.122-0.02010.15410.04510.02680.23870.02170.1566113.473-25.79271.6577
4-0.0263-0.214-0.11360.70550.04841.4080.02610.19590.0961-0.10120.11160.0654-0.0649-0.3158-0.13020.2909-0.03020.0210.85150.00890.4581100.754-28.379222.977
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D

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