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- PDB-8oy7: Time-resolved SFX structure of the class II photolyase complexed ... -

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Basic information

Entry
Database: PDB / ID: 8oy7
TitleTime-resolved SFX structure of the class II photolyase complexed with a thymine dimer (10 nanosecond 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


deoxyribodipyrimidine photo-lyase / deoxyribodipyrimidine photo-lyase activity / DNA repair / 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: 2.36 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
Water3,819212
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 area5530 Å2
ΔGint-37 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 area5150 Å2
ΔGint-24 kcal/mol
Surface area20610 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: 4256.767 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, 215 molecules

#4: Chemical ChemComp-FDA / DIHYDROFLAVINE-ADENINE DINUCLEOTIDE


Mass: 787.566 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H35N9O15P2
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 212 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.69 Å3/Da / Density % sol: 54.19 %
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: 2.36→31.29 Å / Num. obs: 58959 / % possible obs: 100 % / Redundancy: 371.356332 % / Biso Wilson estimate: 32.91 Å2 / CC1/2: 0.9829549 / CC star: 0.9956928 / R split: 0.1154 / Net I/σ(I): 8.086315 / Num. measured all: 21894798
Reflection shell

% possible all: 100

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique allNum. unique obsCC1/2CC starR split
5.0787-6.38981882.324.93302330230.9925720.9981340.05
4.4385-5.07871623.625.38301330130.9903840.9975820.051
4.0339-4.43851436.523.82296529650.9931030.9982680.052
3.7453-4.03391350.621.57297229720.9925330.9981250.054
3.5236-3.74531260.416.67293329330.9855040.9963430.08
3.3478-3.52361189.316.55293829380.9908070.9976890.066
3.202-3.34781111.213.12294729470.9900430.9974950.078
3.0788-3.2021027.510.07294929490.9870390.9967330.097
2.9727-3.0788934.68.3293329330.9828470.9956650.121
2.8802-2.9727842.86.18292529250.9686970.9920180.167
2.798-2.8802746.65.38288628860.9648350.9910110.19
2.7241-2.798654.74.39294729470.9562070.9887430.229
2.6575-2.7241534.83.62292429240.9315920.9821330.279
2.5974-2.6575425.33.08288128810.9148640.9775170.328
2.5419-2.5974338.12.51293029300.8750050.9660930.411
2.4913-2.5419268.32289128910.8147830.9475970.518
2.4444-2.4913221.31.49292329230.6814030.9002870.775
2.401-2.44441791.14289328930.6778450.8988850.934
2.3602-2.401150.90.85289028900.5792150.8564741.228

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.36→31.29 Å / SU ML: 0.4886 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 46.9603
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.4102 2447 5.07 %
Rwork0.3221 45818 -
obs0.3266 48265 82.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.96 Å2
Refinement stepCycle: LAST / Resolution: 2.36→31.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7177 1098 111 212 8598
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01068734
X-RAY DIFFRACTIONf_angle_d1.195112059
X-RAY DIFFRACTIONf_chiral_restr0.05791254
X-RAY DIFFRACTIONf_plane_restr0.00981377
X-RAY DIFFRACTIONf_dihedral_angle_d21.61643370
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.36-2.410.2495110.5329291X-RAY DIFFRACTION8.9
2.41-2.460.6036580.47261056X-RAY DIFFRACTION33.11
2.46-2.520.5392740.45481442X-RAY DIFFRACTION44.55
2.52-2.580.4836970.43751867X-RAY DIFFRACTION57.41
2.58-2.650.51381090.42112284X-RAY DIFFRACTION70.78
2.65-2.730.5061510.42662692X-RAY DIFFRACTION82.77
2.73-2.820.55681520.43253204X-RAY DIFFRACTION98.1
2.82-2.920.49771630.43123268X-RAY DIFFRACTION99.97
2.92-3.040.47071770.41373244X-RAY DIFFRACTION99.91
3.04-3.180.50241920.38293233X-RAY DIFFRACTION100
3.18-3.340.51232010.36993255X-RAY DIFFRACTION100
3.34-3.550.42071410.32023281X-RAY DIFFRACTION99.97
3.55-3.830.41981660.28563288X-RAY DIFFRACTION100
3.83-4.210.33121860.27073286X-RAY DIFFRACTION99.94
4.21-4.820.3531950.25183301X-RAY DIFFRACTION100
4.82-6.060.37021780.2673350X-RAY DIFFRACTION100
6.06-31.290.31451960.25093476X-RAY DIFFRACTION99.32
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)
11.38513787561-0.0363894020788-0.07104879858982.470150966630.3714456924052.46845590438-0.09029252437070.04202392630630.163428520611-0.2709743059160.136667363214-0.03289046870330.2639768228890.2245409763470.0489576495323-0.09344244998810.04247826376040.01863510730850.114057505822-0.01427919434730.13638513620418.490919188316.8470529654-6.19463588255
21.237427579570.844348602562-0.05126783337942.51415005929-0.3379361789421.342821823770.02840453153650.229315178624-0.1887253670310.2199996608340.164669865431-0.009151065575970.7090115510990.0596066246634-0.09668502198350.7205911400730.0822732262607-0.04840504197790.242820086752-0.05277275283980.20183694762210.1914530289-19.1145380086-24.4176536733
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 - G4 - 14
22chain 'B' or chain 'F' or chain 'E'B - FD - I3 - 14

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