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- PDB-8oy9: Time-resolved SFX structure of the class II photolyase complexed ... -

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Basic information

Entry
Database: PDB / ID: 8oy9
TitleTime-resolved SFX structure of the class II photolyase complexed with a thymine dimer (1 microsecond pump-probe delay)
Components
  • COUNTERSTRAND-OLIGONUCLEOTIDE
  • CPD-COMPRISING OLIGONUCLEOTIDE
  • Deoxyribodipyrimidine photo-lyasePhotolyase
KeywordsLYASE / DNA binding protein / DNA repair enzyme / flavoprotein / photoenzyme
Function / homology
Function and homology information


deoxyribodipyrimidine photo-lyase / deoxyribodipyrimidine photo-lyase activity / nucleotide binding / DNA repair / 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: 2.24 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
Water3,207178
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 area5500 Å2
ΔGint-40 kcal/mol
Surface area21860 Å2
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
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5150 Å2
ΔGint-15 kcal/mol
Surface area20370 Å2
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 / Photolyase / 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, 181 molecules

#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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 / Water


Mass: 18.015 Da / Num. of mol.: 178 / 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: 2.24→31.29 Å / Num. obs: 68821 / % possible obs: 100 % / Redundancy: 920.008646 % / Biso Wilson estimate: 36.07 Å2 / CC1/2: 0.9889675 / CC star: 0.9972227 / R split: 0.0901 / Net I/σ(I): 9.496358 / Num. measured all: 63315915
Reflection shell

% possible all: 100

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique allNum. unique obsCC1/2CC starR split
4.8216-6.0682756.427.16352835280.9928480.9982040.046
4.2123-4.82162360.327.35349934990.9910060.9977390.047
3.8285-4.21232127.125.99346534650.9951630.9987870.046
3.5549-3.82851984.624345434540.993790.9984410.048
3.3456-3.55491862.519.66342434240.9918870.9979610.057
3.1776-3.34561742.415.04344134410.9923230.9980720.067
3.0395-3.17761623.312.82344134410.991650.9979020.075
2.9223-3.03951486.710.15341734170.9881630.9970190.099
2.8217-2.92231353.58.14342634260.9829760.9956980.119
2.7337-2.82171199.86.76340934090.9814140.9952990.141
2.6553-2.73371005.75.47342234220.9676780.9917530.182
2.586-2.6553791.74.66339133910.9618290.9902240.214
2.5227-2.586609.53.73341834180.9373030.9836850.279
2.4655-2.5227450.62.97341534150.9170880.9781360.34
2.4131-2.4655327.12.27336933690.9073880.9754210.434
2.3646-2.4131230.21.74339533950.819070.9489660.598
2.3202-2.36461581.38338633860.7443570.9238210.756
2.2784-2.3202111.21.01338133810.5674730.8509181.076
2.2401-2.2784860.65342434240.3925810.7508781.679
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: 2.24→31.29 Å / SU ML: 0.5619 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 48.0926
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3833 2781 5.05 %
Rwork0.3119 52290 -
obs0.3156 55071 80.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 53.67 Å2
Refinement stepCycle: LAST / Resolution: 2.24→31.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7155 1077 111 178 8521
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01018674
X-RAY DIFFRACTIONf_angle_d1.087611969
X-RAY DIFFRACTIONf_chiral_restr0.05651246
X-RAY DIFFRACTIONf_plane_restr0.01021366
X-RAY DIFFRACTIONf_dihedral_angle_d20.83553344
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.24-2.280.6234100.4636174X-RAY DIFFRACTION5.43
2.28-2.320.4266220.4519480X-RAY DIFFRACTION14.9
2.32-2.370.5154550.44871025X-RAY DIFFRACTION32.05
2.37-2.410.5066740.44111433X-RAY DIFFRACTION44.44
2.41-2.470.57371020.45351877X-RAY DIFFRACTION58.83
2.47-2.520.49761170.45972307X-RAY DIFFRACTION71.06
2.52-2.590.49321470.47072626X-RAY DIFFRACTION81.46
2.59-2.660.54351320.47313027X-RAY DIFFRACTION93.63
2.66-2.740.61121760.50153245X-RAY DIFFRACTION99.94
2.74-2.820.5381560.48643238X-RAY DIFFRACTION99.88
2.82-2.920.54341650.47183247X-RAY DIFFRACTION99.97
2.92-3.040.57031730.44563249X-RAY DIFFRACTION99.91
3.04-3.180.48821950.39853224X-RAY DIFFRACTION100
3.18-3.350.41162000.31913230X-RAY DIFFRACTION100
3.35-3.560.3541360.29713279X-RAY DIFFRACTION100
3.56-3.830.37321670.26743280X-RAY DIFFRACTION100
3.83-4.220.32241850.23733261X-RAY DIFFRACTION99.94
4.22-4.820.28591960.22223296X-RAY DIFFRACTION100
4.82-6.070.33011770.23833339X-RAY DIFFRACTION100
6.07-31.290.26291960.21473453X-RAY DIFFRACTION99.02
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)
11.533171960330.03373908313770.06108120137742.857401973380.3412207637832.26619671595-0.1445484475660.05138958365450.148806513055-0.2029911987160.110526465042-0.1121356613530.1845622857090.1782076907370.06668515807350.06435324046590.01962197830620.012032835670.220252541773-0.03447738444670.2070616082718.608735958916.9089098635-6.23437601776
21.491412753031.020308672210.009947575923782.3579023843-0.1460706102471.71101165130.03092893034940.170507916192-0.2302382177940.1959440044990.118516236255-8.06604231024E-50.6881342454430.070905929822-0.09336333799080.7632142305690.0421864648987-0.008225444904210.281864321768-0.05338452607050.27931876331810.1216278255-19.0795152545-24.4128130678
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 - G2 - 14
22chain 'B' or chain 'F' or chain 'E'B - FD - I3 - 13

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