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- PDB-7yel: TR-SFX MmCPDII-DNA complex: 25 us time-point collected in SACLA. ... -

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Basic information

Entry
Database: PDB / ID: 7yel
TitleTR-SFX MmCPDII-DNA complex: 25 us time-point collected in SACLA. Includes 25 us, dark, and extrapolated structure factors
Components
  • (CPD photolesion containing DNA after ...) x 2
  • 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: 2.5 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 6, 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 after repair
D: complementary oligonucleotide to the CPD containing DNA
E: CPD photolesion containing DNA after repair
F: complementary oligonucleotide to the CPD containing DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,4139
Polymers126,7466
Non-polymers1,6673
Water4,882271
1
A: Deoxyribodipyrimidine photo-lyase
C: CPD photolesion containing DNA after repair
D: complementary oligonucleotide to the CPD containing DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,2545
Polymers63,3733
Non-polymers8822
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5130 Å2
ΔGint-40 kcal/mol
Surface area21590 Å2
MethodPISA
2
B: Deoxyribodipyrimidine photo-lyase
E: CPD photolesion containing DNA after repair
F: complementary oligonucleotide to the CPD containing DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,1584
Polymers63,3733
Non-polymers7861
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5630 Å2
ΔGint-18 kcal/mol
Surface area20480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.530, 115.710, 169.280
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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CPD photolesion containing DNA after ... , 2 types, 2 molecules CE

#2: DNA chain CPD photolesion containing DNA after repair


Mass: 3943.560 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain CPD photolesion containing DNA after repair


Mass: 3943.561 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Protein / DNA chain , 2 types, 4 molecules ABDF

#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
#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, 274 molecules

#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: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 271 / 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: 2.99 Å3/Da / Density % sol: 58.84 %
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: SACLA / Beamline: BL2 / Wavelength: 1.0875 Å
DetectorType: MPCCD / Detector: CCD / Date: May 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0875 Å / Relative weight: 1
ReflectionResolution: 2.5→34.61 Å / Num. obs: 50128 / % possible obs: 100 % / Redundancy: 311.51 % / CC1/2: 0.98 / Net I/σ(I): 7.47
Reflection shellResolution: 2.5→2.52 Å / Redundancy: 178.4 % / Mean I/σ(I) obs: 2.39 / Num. unique obs: 2434 / CC1/2: 0.772
Serial crystallography sample deliveryMethod: injection
Serial crystallography sample delivery injectionCarrier solvent: grease / Filter size: 20 µm / Flow rate: 3 µL/min / Injector diameter: 75 µm / Injector temperature: 293 K / Power by: gas
Serial crystallography data reductionFrames indexed: 25079

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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: 7YDZ

7ydz


Resolution: 2.5→34.16 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 34.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2346 2420 4.84 %
Rwork0.2185 --
obs0.2193 50047 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→34.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7041 1092 111 271 8515
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0058674
X-RAY DIFFRACTIONf_angle_d0.78412026
X-RAY DIFFRACTIONf_dihedral_angle_d20.8583219
X-RAY DIFFRACTIONf_chiral_restr0.0471268
X-RAY DIFFRACTIONf_plane_restr0.0071356
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.550.53611510.50172713X-RAY DIFFRACTION100
2.55-2.610.47471430.48382783X-RAY DIFFRACTION100
2.61-2.670.48171440.48022756X-RAY DIFFRACTION100
2.67-2.730.47891480.46172761X-RAY DIFFRACTION100
2.73-2.810.47741390.44152754X-RAY DIFFRACTION100
2.81-2.890.38341520.43112781X-RAY DIFFRACTION100
2.89-2.980.38931230.39132770X-RAY DIFFRACTION100
2.98-3.090.41321380.3572785X-RAY DIFFRACTION100
3.09-3.210.39151620.34332754X-RAY DIFFRACTION100
3.21-3.360.31591260.29642828X-RAY DIFFRACTION100
3.36-3.540.27831220.26652796X-RAY DIFFRACTION100
3.54-3.760.21071520.21292780X-RAY DIFFRACTION100
3.76-4.050.19991170.18482864X-RAY DIFFRACTION100
4.05-4.450.19491300.14672827X-RAY DIFFRACTION100
4.45-5.10.14061910.12982786X-RAY DIFFRACTION100
5.1-6.410.13711300.11692894X-RAY DIFFRACTION100
6.42-34.160.07171520.07112995X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -21.7928 Å / Origin y: -1.0875 Å / Origin z: -15.0978 Å
111213212223313233
T0.2826 Å20.0206 Å20.0113 Å2-0.2977 Å2-0.0009 Å2--0.3027 Å2
L0.2586 °20.0988 °20.0382 °2-0.4398 °20.1013 °2--0.2733 °2
S-0.0127 Å °0.0455 Å °-0.0873 Å °-0.0508 Å °0.0157 Å °-0.0147 Å °0.056 Å °-0.0034 Å °-0.0133 Å °
Refinement TLS groupSelection details: all

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