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- PDB-7ayv: X-ray crystallographic structure of (6-4)photolyase from Drosophi... -

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Basic information

Entry
Database: PDB / ID: 7ayv
TitleX-ray crystallographic structure of (6-4)photolyase from Drosophila melanogaster at cryogenic temperature
ComponentsRE11660p
KeywordsLYASE / 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: 1.79 Å
AuthorsCellini, A. / Wahlgren, W.Y. / Henry, L. / Westenhoff, S.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Swedish Research Council Sweden
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2021
Title: The three-dimensional structure of Drosophila melanogaster (6-4) photolyase at room temperature.
Authors: Cellini, A. / Yuan Wahlgren, W. / Henry, L. / Pandey, S. / Ghosh, S. / Castillon, L. / Claesson, E. / Takala, H. / Kubel, J. / Nimmrich, A. / Kuznetsova, V. / Nango, E. / Iwata, S. / Owada, ...Authors: Cellini, A. / Yuan Wahlgren, W. / Henry, L. / Pandey, S. / Ghosh, S. / Castillon, L. / Claesson, E. / Takala, H. / Kubel, J. / Nimmrich, A. / Kuznetsova, V. / Nango, E. / Iwata, S. / Owada, S. / Stojkovic, E.A. / Schmidt, M. / Ihalainen, J.A. / Westenhoff, S.
History
DepositionNov 13, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 18, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 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)59,6718
Polymers58,3131
Non-polymers1,3587
Water4,558253
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2470 Å2
ΔGint-76 kcal/mol
Surface area21470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.903, 88.933, 114.022
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein RE11660p


Mass: 58313.043 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 K-12 (bacteria) / References: UniProt: Q8SXK5
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 253 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.6 Å3/Da / Density % sol: 52.75 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M Lithium sulphate, 0.1 M Bis-Tris(pH=6.5), 25%PEG3350, 4% polypropylene glycol p 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.9184 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.79→29.42 Å / Num. obs: 58656 / % possible obs: 99.2 % / Redundancy: 12.7 % / Biso Wilson estimate: 25.32 Å2 / CC1/2: 0.99 / Net I/σ(I): 16.9
Reflection shellResolution: 1.79→1.854 Å / Num. unique obs: 3836 / CC1/2: 0.83

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Processing

Software
NameVersionClassification
PHENIX1.17.1-3660-000refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3cvy

3cvy


Resolution: 1.79→29.42 Å / SU ML: 0.2196 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.858
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2062 1997 3.41 %
Rwork0.1761 56572 -
obs0.1771 58569 99.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.96 Å2
Refinement stepCycle: LAST / Resolution: 1.79→29.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4167 0 31 253 4451
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01494320
X-RAY DIFFRACTIONf_angle_d1.2055873
X-RAY DIFFRACTIONf_chiral_restr0.0816608
X-RAY DIFFRACTIONf_plane_restr0.0095746
X-RAY DIFFRACTIONf_dihedral_angle_d7.9472600
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.79-1.830.35171250.31083550X-RAY DIFFRACTION88.7
1.83-1.880.2991420.24234007X-RAY DIFFRACTION99.95
1.88-1.940.22251420.20864018X-RAY DIFFRACTION99.9
1.94-20.24191420.17974019X-RAY DIFFRACTION99.98
2-2.070.22591430.18124058X-RAY DIFFRACTION99.98
2.07-2.160.21121420.17344033X-RAY DIFFRACTION100
2.16-2.260.2211420.17864045X-RAY DIFFRACTION100
2.26-2.370.20791420.16954029X-RAY DIFFRACTION99.98
2.37-2.520.20831430.16754065X-RAY DIFFRACTION99.98
2.52-2.720.20041430.18454073X-RAY DIFFRACTION100
2.72-2.990.23831450.19644089X-RAY DIFFRACTION100
2.99-3.420.2141450.19434107X-RAY DIFFRACTION100
3.42-4.310.18141470.1524162X-RAY DIFFRACTION100
4.31-29.420.17151540.15354317X-RAY DIFFRACTION99.91
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)
10.07371320603650.05400609054530.08723482111030.06992081582990.03334573117580.081149933412-0.07557372147460.01467978983430.04075216611280.1035776487170.06412708742690.04886488448460.00571780345528-0.0750440661448-9.00160061931E-60.1731644858560.01205988040880.01474535028520.2033347139770.006053459080540.190007569746-20.782299834420.1724968045-11.3518313344
20.640025764802-0.40046625574-0.2194424292340.6669309319120.1653092648780.524580372979-0.0663106568731-0.0510796423547-0.09209010162440.0980183694620.0847341079828-0.02818726111430.03555259337650.0951519877093-0.0001155925827660.1836066613560.0144879206821-0.01814788439380.167991594104-0.009664010096850.1811179300411.5467413417-7.0494828049-12.0144921929
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 33 )
2X-RAY DIFFRACTION2chain 'A' and (resid 296 through 504 )

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