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- PDB-7yd7: TR-SFX MmCPDII-DNA complex: 1 ns snapshot. Includes 1 ns, dark, a... -

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Basic information

Entry
Database: PDB / ID: 7yd7
TitleTR-SFX MmCPDII-DNA complex: 1 ns snapshot. Includes 1 ns, dark, and extrapolated structure factors
Components
  • CPD photolesion containing DNA
  • Deoxyribodipyrimidine photo-lyase
  • complementary oligonucleotide to the CPD containing DNA
KeywordsDNA BINDING PROTEIN / Flavoprotein / photolyase / light driven electron transfer / DNA repair / time-resolved serial crystallography.
Function / homology
Function and homology information


deoxyribodipyrimidine photo-lyase / deoxyribodipyrimidine photo-lyase activity / 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
FLAVIN-ADENINE DINUCLEOTIDE / DNA / DNA (> 10) / Deoxyribodipyrimidine photo-lyase
Similarity search - Component
Biological speciesMethanosarcina mazei (archaea)
synthetic construct (others)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsMaestre-Reyna, M. / Wang, P.-H. / Nango, E. / Hosokawa, Y. / Saft, M. / Furrer, A. / Yang, C.-H. / Ngura Putu, E.P.G. / Wu, W.-J. / Emmerich, H.-J. ...Maestre-Reyna, M. / Wang, P.-H. / Nango, E. / Hosokawa, Y. / Saft, M. / Furrer, A. / Yang, C.-H. / Ngura Putu, E.P.G. / Wu, W.-J. / Emmerich, H.-J. / Engilberge, S. / Caramello, N. / Wranik, M. / Glover, H.L. / Franz-Badur, S. / Wu, H.-Y. / Lee, C.-C. / Huang, W.-C. / Huang, K.-F. / Chang, Y.-K. / Liao, J.-H. / Weng, J.-H. / Gad, W. / Chang, C.-W. / Pang, A.H. / Gashi, D. / Beale, E. / Ozerov, D. / Milne, C. / Cirelli, C. / Bacellar, C. / Sugahara, M. / Owada, S. / Joti, Y. / Yamashita, A. / Tanaka, R. / Tanaka, T. / Luo, F.J. / Tono, K. / Kiontke, S. / Spadaccini, R. / Royant, A. / Yamamoto, J. / Iwata, S. / Standfuss, J. / Essen, L.-O. / Bessho, Y. / Tsai, M.-D.
Funding support Taiwan, Japan, 3items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan)AS-KPQ-105-TPP Taiwan
Ministry of Science and Technology (MoST, Taiwan)AS-KPQ-109-TPP2 Taiwan
Japan Society for the Promotion of Science (JSPS)16K01942 Japan
CitationJournal: Science / Year: 2023
Title: Visualizing the DNA repair process by a photolyase at atomic resolution.
Authors: Maestre-Reyna, M. / Wang, P.H. / Nango, E. / Hosokawa, Y. / Saft, M. / Furrer, A. / Yang, C.H. / Gusti Ngurah Putu, E.P. / Wu, W.J. / Emmerich, H.J. / Caramello, N. / Franz-Badur, S. / Yang, ...Authors: Maestre-Reyna, M. / Wang, P.H. / Nango, E. / Hosokawa, Y. / Saft, M. / Furrer, A. / Yang, C.H. / Gusti Ngurah Putu, E.P. / Wu, W.J. / Emmerich, H.J. / Caramello, N. / Franz-Badur, S. / Yang, C. / Engilberge, S. / Wranik, M. / Glover, H.L. / Weinert, T. / Wu, H.Y. / Lee, C.C. / Huang, W.C. / Huang, K.F. / Chang, Y.K. / Liao, J.H. / Weng, J.H. / Gad, W. / Chang, C.W. / Pang, A.H. / Yang, K.C. / Lin, W.T. / Chang, Y.C. / Gashi, D. / Beale, E. / Ozerov, D. / Nass, K. / Knopp, G. / Johnson, P.J.M. / Cirelli, C. / Milne, C. / Bacellar, C. / Sugahara, M. / Owada, S. / Joti, Y. / Yamashita, A. / Tanaka, R. / Tanaka, T. / Luo, F. / Tono, K. / Zarzycka, W. / Muller, P. / Alahmad, M.A. / Bezold, F. / Fuchs, V. / Gnau, P. / Kiontke, S. / Korf, L. / Reithofer, V. / Rosner, C.J. / Seiler, E.M. / Watad, M. / Werel, L. / Spadaccini, R. / Yamamoto, J. / Iwata, S. / Zhong, D. / Standfuss, J. / Royant, A. / Bessho, Y. / Essen, L.O. / Tsai, M.D.
History
DepositionJul 4, 2022Deposition site: PDBJ / Processing site: PDBJ
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
Revision 1.2Mar 13, 2024Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id

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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 photolesion containing DNA
D: complementary oligonucleotide to the CPD containing DNA
E: CPD photolesion containing DNA
F: complementary oligonucleotide to the CPD containing DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,0399
Polymers127,3726
Non-polymers1,6673
Water7,116395
1
A: Deoxyribodipyrimidine photo-lyase
C: CPD photolesion containing DNA
D: complementary oligonucleotide to the CPD containing DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,5685
Polymers63,6863
Non-polymers8822
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5680 Å2
ΔGint-36 kcal/mol
Surface area21420 Å2
MethodPISA
2
B: Deoxyribodipyrimidine photo-lyase
E: CPD photolesion containing DNA
F: complementary oligonucleotide to the CPD containing DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,4724
Polymers63,6863
Non-polymers7861
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5570 Å2
ΔGint-16 kcal/mol
Surface area20210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.470, 115.930, 169.350
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Deoxyribodipyrimidine photo-lyase / DNA photolyase


Mass: 55123.480 Da / Num. of mol.: 2 / Mutation: M377T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanosarcina mazei (archaea)
Strain: ATCC BAA-159 / DSM 3647 / Goe1 / Go1 / JCM 11833 / OCM 88
Gene: DU34_19720, DU35_15210, DU36_16165, DU37_08235, DU38_17340, DU39_00605, DU41_17975, DU42_05505, DU44_19145, DU46_16260, DU48_13210, DU49_01325, DU51_15440, DU57_04540, DU59_03190, DU60_01690, ...Gene: DU34_19720, DU35_15210, DU36_16165, DU37_08235, DU38_17340, DU39_00605, DU41_17975, DU42_05505, DU44_19145, DU46_16260, DU48_13210, DU49_01325, DU51_15440, DU57_04540, DU59_03190, DU60_01690, DU61_08490, DU62_04430, DU63_10745, DU65_18915, DU69_04700, DU71_05355, DU72_08110, DU74_09110, FQU78_02295
Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A0F8I5V2, deoxyribodipyrimidine photo-lyase

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DNA chain , 2 types, 4 molecules CEDF

#2: DNA chain CPD photolesion containing DNA


Mass: 4256.768 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain complementary oligonucleotide to the CPD containing DNA


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, 398 molecules

#4: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 395 / 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: 2.78 Å3/Da / Density % sol: 55.74 %
Crystal growTemperature: 296 K / Method: batch mode / pH: 4.6
Details: 100 mM Sodium Acetate pH 4.6 250 mM ammonium sulfate 4% PEG4000 (w/v) 50 mM DTT

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SwissFEL ARAMIS / Beamline: ESA / Wavelength: 1.0875 Å
DetectorType: PSI JUNGFRAU 16M / Detector: PIXEL / Date: Sep 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0875 Å / Relative weight: 1
ReflectionResolution: 2.15→16.76 Å / Num. obs: 78215 / % possible obs: 99.99 % / Redundancy: 1251.1 % / CC1/2: 0.996 / Net I/σ(I): 11.65
Reflection shellResolution: 2.15→2.17 Å / Redundancy: 790.6 % / Mean I/σ(I) obs: 2.5 / Num. unique obs: 3870 / CC1/2: 0.678 / % possible all: 100
Serial crystallography measurementXFEL pulse repetition rate: 100 Hz
Serial crystallography sample deliveryMethod: injection
Serial crystallography sample delivery injectionDescription: SwissFEL injector / Filter size: 20 µm / Flow rate: 4.2 µL/min / Injector diameter: 75 µm / Injector temperature: 298 K
Serial crystallography data reductionFrames indexed: 86358

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
CrystFELdata reduction
pointlessdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7YC7

7yc7


Resolution: 2.25→16.76 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 30.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2482 3351 4.91 %
Rwork0.2314 --
obs0.2322 68289 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.25→16.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7054 1021 111 395 8581
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0168687
X-RAY DIFFRACTIONf_angle_d0.72612056
X-RAY DIFFRACTIONf_dihedral_angle_d19.6191533
X-RAY DIFFRACTIONf_chiral_restr0.1161274
X-RAY DIFFRACTIONf_plane_restr0.0081378
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.280.51731460.43252670X-RAY DIFFRACTION100
2.28-2.320.45821450.41782680X-RAY DIFFRACTION100
2.32-2.350.41451650.4092632X-RAY DIFFRACTION100
2.35-2.390.45021320.4022677X-RAY DIFFRACTION100
2.39-2.430.44971680.39412639X-RAY DIFFRACTION100
2.43-2.480.42721170.40232693X-RAY DIFFRACTION100
2.48-2.520.40051320.39232673X-RAY DIFFRACTION100
2.52-2.570.42061450.37672682X-RAY DIFFRACTION100
2.57-2.630.38791360.37392691X-RAY DIFFRACTION100
2.63-2.690.31641470.36672676X-RAY DIFFRACTION100
2.69-2.760.37081280.3292693X-RAY DIFFRACTION100
2.76-2.830.33511480.33592660X-RAY DIFFRACTION100
2.83-2.920.35191350.31662699X-RAY DIFFRACTION100
2.92-3.010.33171230.28452694X-RAY DIFFRACTION100
3.01-3.120.30881540.27722699X-RAY DIFFRACTION100
3.12-3.240.27551420.26852682X-RAY DIFFRACTION100
3.24-3.390.2421150.24072739X-RAY DIFFRACTION100
3.39-3.560.20271290.20972712X-RAY DIFFRACTION100
3.56-3.780.18131440.18292731X-RAY DIFFRACTION100
3.78-4.070.16621110.15852739X-RAY DIFFRACTION100
4.07-4.470.16061330.14132762X-RAY DIFFRACTION100
4.48-5.110.12841820.12412712X-RAY DIFFRACTION100
5.11-6.370.15791250.12792808X-RAY DIFFRACTION100
6.37-16.760.09541490.09212895X-RAY DIFFRACTION100

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