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- PDB-8c69: Light SFX structure of D.m(6-4)photolyase at 100 microsecond time... -

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Basic information

Entry
Database: PDB / ID: 8c69
TitleLight SFX structure of D.m(6-4)photolyase at 100 microsecond time delay
ComponentsCryptochrome-1
KeywordsFLAVOPROTEIN / photolyase / SFX / FAD
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: 1.9 Å
AuthorsCellini, A. / Kumar, M. / Nimmrich, A. / Mutisya, J. / Furrer, A. / Beale, E.V. / Carrillo, M. / Malla, T.N. / Maj, P. / Dworkowskic, F. ...Cellini, A. / Kumar, M. / Nimmrich, A. / Mutisya, J. / Furrer, A. / Beale, E.V. / Carrillo, M. / Malla, T.N. / Maj, P. / Dworkowskic, F. / Cirelli, C. / Ozerovi, D. / Bacellar, C. / Strandfuss, J. / Weinert, T. / Ihalainen, J.A. / Yuan Wahlgren, W. / Westenhoff, S.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)European Union
CitationJournal: Nat.Chem. / Year: 2024
Title: Directed ultrafast conformational changes accompany electron transfer in a photolyase as resolved by serial crystallography.
Authors: Cellini, A. / Shankar, M.K. / Nimmrich, A. / Hunt, L.A. / Monrroy, L. / Mutisya, J. / Furrer, A. / Beale, E.V. / Carrillo, M. / Malla, T.N. / Maj, P. / Vrhovac, L. / Dworkowski, F. / ...Authors: Cellini, A. / Shankar, M.K. / Nimmrich, A. / Hunt, L.A. / Monrroy, L. / Mutisya, J. / Furrer, A. / Beale, E.V. / Carrillo, M. / Malla, T.N. / Maj, P. / Vrhovac, L. / Dworkowski, F. / Cirelli, C. / Johnson, P.J.M. / Ozerov, D. / Stojkovic, E.A. / Hammarstrom, L. / Bacellar, C. / Standfuss, J. / Maj, M. / Schmidt, M. / Weinert, T. / Ihalainen, J.A. / Wahlgren, W.Y. / Westenhoff, S.
History
DepositionJan 11, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 1, 2023Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cryptochrome-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,9573
Polymers58,0801
Non-polymers8782
Water2,414134
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1520 Å2
ΔGint-8 kcal/mol
Surface area21330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.900, 103.900, 52.190
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 Cryptochrome-1


Mass: 58079.805 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 (E. coli) / References: UniProt: Q8SXK5
#2: Chemical ChemComp-FAD / 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
#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.: 134 / 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: 2.43 Å3/Da / Density % sol: 49.28 %
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 / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SwissFEL ARAMIS / Beamline: ESA / Wavelength: 1 Å
DetectorType: PSI JUNGFRAU 16M / Detector: PIXEL / Date: Sep 26, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→15.72 Å / Num. obs: 44135 / % possible obs: 99.99 % / Redundancy: 88.9 % / Biso Wilson estimate: 4.81 Å2 / R split: 0.11 / Net I/σ(I): 8.76
Reflection shellResolution: 1.9→1.91 Å / Num. unique obs: 1766 / R split: 0.41
Serial crystallography sample deliveryMethod: injection

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→15.72 Å / SU ML: 0.2878 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 30.2025
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2998 2101 4.97 %
Rwork0.2627 40148 -
obs0.2646 42249 95.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.55 Å2
Refinement stepCycle: LAST / Resolution: 1.9→15.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4099 0 59 134 4292
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00764285
X-RAY DIFFRACTIONf_angle_d0.87125824
X-RAY DIFFRACTIONf_chiral_restr0.0497607
X-RAY DIFFRACTIONf_plane_restr0.0083743
X-RAY DIFFRACTIONf_dihedral_angle_d15.66381627
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.940.37571210.34752434X-RAY DIFFRACTION87.5
1.94-1.990.38821150.33632500X-RAY DIFFRACTION89.52
1.99-2.050.381140.32472556X-RAY DIFFRACTION91.31
2.05-2.110.38031690.30932542X-RAY DIFFRACTION92.68
2.11-2.170.36211290.29372620X-RAY DIFFRACTION94.56
2.17-2.250.32961220.28462685X-RAY DIFFRACTION96.13
2.25-2.340.28231460.27732681X-RAY DIFFRACTION96.62
2.34-2.450.32731520.26612660X-RAY DIFFRACTION96.53
2.45-2.580.30091630.27022698X-RAY DIFFRACTION97.11
2.58-2.740.36041560.29682734X-RAY DIFFRACTION97.9
2.74-2.950.31741150.29232780X-RAY DIFFRACTION98.81
2.95-3.240.31481400.31492770X-RAY DIFFRACTION98.95
3.24-3.70.27561720.25122788X-RAY DIFFRACTION99.8
3.71-4.650.18841480.16492808X-RAY DIFFRACTION99.76
4.65-15.720.1821390.14742892X-RAY DIFFRACTION99.54
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)
16.00495781934E-6-0.00174550123804-0.0005703825988220.0008775588156850.0005477996904479.51913635452E-5-0.00170936970147-0.00402777088927-0.006361142745390.00147402177540.002380865724710.00557554205318-0.000131958050672-0.003414514712484.15168632477E-100.01551608815070.00172120290459-0.003653496644760.0190638888223-0.001295572919530.020354002969119.706773132441.7163125044.37483082644
2-0.0007714182704890.00058768107486-0.000183068725473-0.0005503529520559.85376789769E-5-0.000572653815132-0.006038441789830.003926764137590.00205401780835-0.000262862970792-0.005200461289980.00422837093592-0.00392530568597-0.00427871041764.72927886073E-100.00114088322002-0.00877542067675-0.0122990725462-0.0253155287197-0.00113513460914-0.0191765622012-4.9643522941625.5611426669-1.27843077615
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 5 through 295 )5 - 2951 - 291
22chain 'A' and (resid 296 through 504 )296 - 504292 - 500

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