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- PDB-8oy3: Time-resolved SFX structure of the class II photolyase complexed ... -

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Basic information

Entry
Database: PDB / ID: 8oy3
TitleTime-resolved SFX structure of the class II photolyase complexed with a thymine dimer (3 picosecond pump-probe delay)
Components
  • COUNTERSTRAND-OLIGONUCLEOTIDE
  • CPD-COMPRISING OLIGONUCLEOTIDE
  • Deoxyribodipyrimidine photo-lyase
KeywordsLYASE / DNA binding protein / DNA repair enzyme / flavoprotein / photoenzyme
Function / homology
Function and homology information


photoreactive repair / deoxyribodipyrimidine photo-lyase / deoxyribodipyrimidine photo-lyase activity / nucleotide binding / DNA binding
Similarity search - Function
DNA photolyase class 2 / : / 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
DIHYDROFLAVINE-ADENINE DINUCLEOTIDE / DNA / DNA (> 10) / Deoxyribodipyrimidine photo-lyase
Similarity search - Component
Biological speciesMethanosarcina mazei Go1 (archaea)
synthetic construct (others)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 2.16 Å
AuthorsLane, T.J. / Christou, N.-E. / Melo, D.V.M. / Apostolopoulou, V. / Pateras, A. / Mashhour, A.R. / Galchenkova, M. / Gunther, S. / Reinke, P. / Kremling, V. ...Lane, T.J. / Christou, N.-E. / Melo, D.V.M. / Apostolopoulou, V. / Pateras, A. / Mashhour, A.R. / Galchenkova, M. / Gunther, S. / Reinke, P. / Kremling, V. / Oberthuer, D. / Henkel, A. / Sprenger, J. / Scheer, T.E.S. / Lange, E. / Yefanov, O.N. / Middendorf, P. / Sellberg, J.A. / Schubert, R. / Fadini, A. / Cirelli, C. / Beale, E.V. / Johnson, P. / Dworkowski, F. / Ozerov, D. / Bertrand, Q. / Wranik, M. / Zitter, E.D. / Turk, D. / Bajt, S. / Chapman, H. / Bacellar, C.
Funding support Germany, Switzerland, 2items
OrganizationGrant numberCountry
Helmholtz Association Germany
Swiss National Science Foundation Switzerland
CitationJournal: Science / Year: 2023
Title: Time-resolved crystallography captures light-driven DNA repair.
Authors: Christou, N.E. / Apostolopoulou, V. / Melo, D.V.M. / Ruppert, M. / Fadini, A. / Henkel, A. / Sprenger, J. / Oberthuer, D. / Gunther, S. / Pateras, A. / Rahmani Mashhour, A. / Yefanov, O.M. / ...Authors: Christou, N.E. / Apostolopoulou, V. / Melo, D.V.M. / Ruppert, M. / Fadini, A. / Henkel, A. / Sprenger, J. / Oberthuer, D. / Gunther, S. / Pateras, A. / Rahmani Mashhour, A. / Yefanov, O.M. / Galchenkova, M. / Reinke, P.Y.A. / Kremling, V. / Scheer, T.E.S. / Lange, E.R. / Middendorf, P. / Schubert, R. / De Zitter, E. / Lumbao-Conradson, K. / Herrmann, J. / Rahighi, S. / Kunavar, A. / Beale, E.V. / Beale, J.H. / Cirelli, C. / Johnson, P.J.M. / Dworkowski, F. / Ozerov, D. / Bertrand, Q. / Wranik, M. / Bacellar, C. / Bajt, S. / Wakatsuki, S. / Sellberg, J.A. / Huse, N. / Turk, D. / Chapman, H.N. / Lane, T.J.
History
DepositionMay 3, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 22, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Deoxyribodipyrimidine photo-lyase
B: Deoxyribodipyrimidine photo-lyase
C: CPD-COMPRISING OLIGONUCLEOTIDE
D: COUNTERSTRAND-OLIGONUCLEOTIDE
E: CPD-COMPRISING OLIGONUCLEOTIDE
F: COUNTERSTRAND-OLIGONUCLEOTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,8769
Polymers131,2056
Non-polymers1,6713
Water4,306239
1
A: Deoxyribodipyrimidine photo-lyase
C: CPD-COMPRISING OLIGONUCLEOTIDE
D: COUNTERSTRAND-OLIGONUCLEOTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,4865
Polymers65,6023
Non-polymers8842
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5940 Å2
ΔGint-36 kcal/mol
Surface area21940 Å2
MethodPISA
2
B: Deoxyribodipyrimidine photo-lyase
E: CPD-COMPRISING OLIGONUCLEOTIDE
F: COUNTERSTRAND-OLIGONUCLEOTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,3904
Polymers65,6023
Non-polymers7881
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5550 Å2
ΔGint-17 kcal/mol
Surface area20840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.200, 117.760, 170.470
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

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Protein , 1 types, 2 molecules AB

#1: Protein Deoxyribodipyrimidine photo-lyase / DNA photolyase


Mass: 57039.734 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanosarcina mazei Go1 (archaea) / Gene: MM_0852 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q8PYK9, deoxyribodipyrimidine photo-lyase

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DNA chain , 2 types, 4 molecules CEDF

#2: DNA chain CPD-COMPRISING OLIGONUCLEOTIDE


Mass: 4256.768 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain COUNTERSTRAND-OLIGONUCLEOTIDE


Mass: 4305.805 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 3 types, 242 molecules

#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-FDA / DIHYDROFLAVINE-ADENINE DINUCLEOTIDE


Mass: 787.566 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H35N9O15P2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 239 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.67 Å3/Da / Density % sol: 53.98 %
Crystal growTemperature: 293 K / Method: batch mode
Details: 100 mM Amm sulfate, 100 mM Acetate pH 4.6, 4% PEG 4000, 10 mM Tris pH 7.5, 75 mM NaCl

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SwissFEL ARAMIS / Beamline: ESA / Wavelength: 1.035 Å
DetectorType: PSI JUNGFRAU 16M / Detector: PIXEL / Date: Jul 2, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.035 Å / Relative weight: 1
ReflectionResolution: 2.16→31.29 Å / Num. obs: 75809 / % possible obs: 98.9312 % / Redundancy: 1387.041024 % / Biso Wilson estimate: 34.8 Å2 / CC1/2: 0.99658 / CC star: 0.9991432 / R split: 0.0577 / Net I/σ(I): 15.996742 / Num. measured all: 105150193
Reflection shell
Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique allNum. unique obsCC1/2CC starR split% possible all
4.649-5.85143294.338.68393539350.9969710.9992410.032100
4.0634-4.6492802.238.76388838880.9965870.9991450.032100
3.6914-4.06342548.637.96385338530.9968110.9992010.033100
3.4282-3.69142360.334.57386238620.9970270.9992550.033100
3.2258-3.42822197.126.72383238320.9970720.9992670.038100
3.0647-3.22582008.922.72382238220.9967360.9991820.043100
2.9308-3.06471795.217.84380038000.9941910.9985430.058100
2.8185-2.93081544.114.11383338330.9935270.9983750.069100
2.7211-2.81851274.111.51380838080.9931260.9982740.083100
2.6364-2.7211923.89.15379637960.9886590.9971440.106100
2.5608-2.6364633.47.31380138010.9841670.9960020.133100
2.4931-2.5608402.75.46379537950.9694770.9922210.185100
2.4325-2.4931244.94.15377037700.9578820.9891850.249100
2.3776-2.4325139.82.95381438140.9143420.9773710.373100
2.3267-2.377678.62.18376137610.8163250.948090.533100
2.28-2.326740.81.52378437840.6649030.8937160.796100
2.2371-2.2822.60.99380137840.470480.7999371.21399.55
2.1973-2.237112.50.82375736380.4146030.7656211.30696.83
2.1598-2.19736.80.65379731140.4511280.7885191.44682.01
Serial crystallography sample deliveryMethod: injection

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.16→31.29 Å / SU ML: 0.4814 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 44.3018
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3352 3069 5.04 %
Rwork0.2731 57870 -
obs0.2763 60939 79.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 54.05 Å2
Refinement stepCycle: LAST / Resolution: 2.16→31.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7160 1077 111 239 8587
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00968713
X-RAY DIFFRACTIONf_angle_d1.073812037
X-RAY DIFFRACTIONf_chiral_restr0.05651253
X-RAY DIFFRACTIONf_plane_restr0.0091385
X-RAY DIFFRACTIONf_dihedral_angle_d20.66453392
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.16-2.20.607940.304491X-RAY DIFFRACTION2.76
2.2-2.230.5286200.366377X-RAY DIFFRACTION11.66
2.23-2.270.4965550.3611827X-RAY DIFFRACTION25.79
2.27-2.310.4222610.35531290X-RAY DIFFRACTION39.86
2.31-2.360.4407890.37211671X-RAY DIFFRACTION51.12
2.36-2.410.50971110.38172122X-RAY DIFFRACTION64.84
2.41-2.460.49071310.40112482X-RAY DIFFRACTION76.63
2.46-2.510.51071320.43762775X-RAY DIFFRACTION84.51
2.51-2.580.50581740.46633138X-RAY DIFFRACTION97.15
2.58-2.650.46441500.45043270X-RAY DIFFRACTION100
2.65-2.720.45961740.48873282X-RAY DIFFRACTION100
2.72-2.810.55131580.46593286X-RAY DIFFRACTION99.97
2.81-2.910.47081640.44443296X-RAY DIFFRACTION99.94
2.91-3.030.57061740.4063254X-RAY DIFFRACTION99.91
3.03-3.170.46071980.34773269X-RAY DIFFRACTION100
3.17-3.330.41571990.30243279X-RAY DIFFRACTION100
3.33-3.540.30191440.25633303X-RAY DIFFRACTION99.97
3.54-3.820.30991670.21613327X-RAY DIFFRACTION100
3.82-4.20.23141910.19513312X-RAY DIFFRACTION99.97
4.2-4.80.23791950.17693318X-RAY DIFFRACTION100
4.81-6.050.26451790.193388X-RAY DIFFRACTION100
6.05-31.290.23531990.19223513X-RAY DIFFRACTION99.65
Refinement TLS params.

L11: 0 °2 / L12: 0 °2 / L13: 0 °2 / L22: 0 °2 / L23: 0 °2 / L33: 0 °2 / S11: 0 Å ° / S12: 0 Å ° / S13: 0 Å ° / S21: 0 Å ° / S22: 0 Å ° / S23: 0 Å ° / S31: 0 Å ° / S32: 0 Å ° / S33: 0 Å ° / T11: 0 Å2 / T12: 0 Å2 / T13: 0 Å2 / T22: 0 Å2 / T23: 0 Å2 / T33: 0 Å2 / Method: refined / Refine-ID: X-RAY DIFFRACTION

IDOrigin x (Å)Origin y (Å)Origin z (Å)
118.44292590316.9103452474-6.39270840923
29.96752289899-19.0233263142-24.5533030463
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Label seq-ID: 1

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-ID
11chain 'A' or chain 'C' or chain 'D'A - DA - G3 - 14
22chain 'B' or chain 'F' or chain 'E'B - FD - I3 - 13

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