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- PDB-7qut: serial synchrotron crystallographic structure of Drosophila Melan... -

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Basic information

Entry
Database: PDB / ID: 7qut
Titleserial synchrotron crystallographic structure of Drosophila Melanogaster (6-4) photolyase
ComponentsRE11660p
KeywordsDNA BINDING PROTEIN / flavoprotein / (6-4)photolyase
Function / homology
Function and homology information


deoxyribodipyrimidine photo-lyase activity / entrainment of circadian clock by photoperiod / FAD binding / circadian regulation of gene expression / DNA binding / nucleus / cytoplasm
Similarity search - Function
Cryptochrome/DNA photolyase class 1 / Cryptochrome/DNA photolyase, FAD-binding domain / FAD binding domain of DNA photolyase / DNA photolyase, N-terminal / Cryptochrome/photolyase, N-terminal domain superfamily / DNA photolyase / Photolyase/cryptochrome alpha/beta domain profile. / Cryptochrome/DNA photolyase, FAD-binding domain-like superfamily / Rossmann-like alpha/beta/alpha sandwich fold
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / RE11660p
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 Å
AuthorsCellini, A. / Weixiao, Y.W. / Kumar, M.S. / Westenhoff, S.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European CommissionMolStuctDynEuropean Union
CitationJournal: Chem.Commun.(Camb.) / Year: 2022
Title: Structural basis of the radical pair state in photolyases and cryptochromes.
Authors: Cellini, A. / Shankar, M.K. / Wahlgren, W.Y. / Nimmrich, A. / Furrer, A. / James, D. / Wranik, M. / Aumonier, S. / Beale, E.V. / Dworkowski, F. / Standfuss, J. / Weinert, T. / Westenhoff, S.
History
DepositionJan 18, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 13, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RE11660p
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,7253
Polymers58,8481
Non-polymers8782
Water1,71195
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1500 Å2
ΔGint-8 kcal/mol
Surface area21250 Å2
Unit cell
Length a, b, c (Å)103.600, 103.600, 52.080
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41
Space group name HallP4w
Symmetry operation#1: x,y,z
#2: -y,x,z+1/4
#3: y,-x,z+3/4
#4: -x,-y,z+1/2

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Components

#1: Protein RE11660p


Mass: 58847.684 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: phr6-4, CG2488 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8SXK5
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / 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: 2.41 Å3/Da / Density % sol: 48.88 %
Crystal growTemperature: 277.15 K / Method: batch mode / pH: 6.5
Details: 100 mM bis-tris pH=6.5, 200 mM lithium sulphate monohydrate, 22 % PEG 3350, 0.5 % Ethyl acetate

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Data collection

DiffractionMean temperature: 293.15 K / Ambient temp details: room temperature / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.3 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 11, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3 Å / Relative weight: 1
ReflectionResolution: 2.24→19.3 Å / Num. obs: 26853 / % possible obs: 100 % / Redundancy: 1948 % / Biso Wilson estimate: 50.38 Å2 / CC1/2: 0.99 / Net I/σ(I): 8.58
Reflection shellResolution: 2.24→2.26 Å / Num. unique obs: 1077 / CC1/2: 0.2
Serial crystallography sample deliveryMethod: injection

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Processing

Software
NameVersionClassification
PHENIX1.19.2-4158refinement
CrystFELdata reduction
CrystFELdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7AYV

7ayv


Resolution: 2.24→19.3 Å / SU ML: 0.344 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.3909
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1911 1407 5.24 %
Rwork0.15 25424 -
obs0.1522 26831 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 59.74 Å2
Refinement stepCycle: LAST / Resolution: 2.24→19.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4099 0 59 95 4253
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00914314
X-RAY DIFFRACTIONf_angle_d1.69515871
X-RAY DIFFRACTIONf_chiral_restr0.1112612
X-RAY DIFFRACTIONf_plane_restr0.0075751
X-RAY DIFFRACTIONf_dihedral_angle_d18.29361643
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.24-2.320.36961480.33492508X-RAY DIFFRACTION99.96
2.32-2.410.33841310.30882534X-RAY DIFFRACTION99.93
2.41-2.520.30921440.27052518X-RAY DIFFRACTION100
2.52-2.650.30051170.23682531X-RAY DIFFRACTION99.96
2.66-2.820.27671500.22522528X-RAY DIFFRACTION100
2.82-3.040.26691230.1842552X-RAY DIFFRACTION100
3.04-3.340.20361330.16212549X-RAY DIFFRACTION100
3.34-3.820.20351660.12762517X-RAY DIFFRACTION99.96
3.82-4.80.12911480.09892561X-RAY DIFFRACTION100
4.8-19.30.13071470.1062626X-RAY DIFFRACTION99.96

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