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

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Basic information

Entry
Database: PDB / ID: 7azt
TitleX-ray crystallographic structure of (6-4)photolyase from Drosophila melanogaster at room 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 / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 2.27 Å
AuthorsCellini, A. / Wahlgren, W.Y. / Henry, L. / Westenhoff, S. / Pandey, 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 17, 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)59,0972
Polymers58,3111
Non-polymers7861
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1240 Å2
ΔGint-7 kcal/mol
Surface area22460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.630, 91.640, 115.970
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: 58310.973 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-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
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: 2.81 Å3/Da / Density % sol: 56.2 %
Crystal growTemperature: 277.15 K / Method: batch mode / pH: 6.5
Details: 0.2 M lithium sulftate, 0.1 M bis-tris (pH=6.5), 25% PEG3350, 4% polypropyle glycol P400

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SACLA / Beamline: BL3 / Wavelength: 1.7712 Å
DetectorType: MPCCD / Detector: CCD / Date: May 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7712 Å / Relative weight: 1
ReflectionResolution: 2.27→42.61 Å / Num. obs: 33953 / % possible obs: 100 % / Redundancy: 106 % / Biso Wilson estimate: 90.69 Å2 / CC1/2: 0.97 / Net I/σ(I): 4.93
Reflection shellResolution: 2.27→2.351 Å / Num. unique obs: 1352 / CC1/2: 0.32
Serial crystallography sample deliveryMethod: injection

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7AYV

7ayv


Resolution: 2.27→42.61 Å / SU ML: 0.3689 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.0904
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2078 1501 4.83 %
Rwork0.1724 29573 -
obs0.1742 31074 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 93.13 Å2
Refinement stepCycle: LAST / Resolution: 2.27→42.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4168 0 0 0 4168
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00684296
X-RAY DIFFRACTIONf_angle_d0.88625840
X-RAY DIFFRACTIONf_chiral_restr0.052608
X-RAY DIFFRACTIONf_plane_restr0.006747
X-RAY DIFFRACTIONf_dihedral_angle_d18.41591632
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.27-2.340.35791210.28462667X-RAY DIFFRACTION100
2.34-2.430.32481370.26922624X-RAY DIFFRACTION100
2.43-2.520.33921420.26822654X-RAY DIFFRACTION100
2.52-2.640.36171510.26452639X-RAY DIFFRACTION100
2.64-2.780.32881200.26182665X-RAY DIFFRACTION100
2.78-2.950.31011400.23622670X-RAY DIFFRACTION100
2.95-3.180.28981330.23422654X-RAY DIFFRACTION100
3.18-3.50.24841410.20562684X-RAY DIFFRACTION100
3.5-4.010.18751250.16612735X-RAY DIFFRACTION100
4.01-5.050.18251390.14922730X-RAY DIFFRACTION100
5.05-42.610.1811520.15212851X-RAY DIFFRACTION99.93

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