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- PDB-8kcm: MmCPDII-DNA complex containing low-dosage, light induced repaired DNA. -

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Basic information

Entry
Database: PDB / ID: 8kcm
TitleMmCPDII-DNA complex containing low-dosage, light induced repaired DNA.
Components
  • Deoxyribodipyrimidine photo-lyasePhotolyase
  • Repaired DNA
  • complementary oligonucleotide to the repaired 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 / SYNCHROTRON / 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
DepositionAug 8, 2023Deposition 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: Repaired DNA
D: complementary oligonucleotide to the repaired DNA
E: Repaired DNA
F: complementary oligonucleotide to the repaired DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,86818
Polymers127,3726
Non-polymers2,49612
Water10,016556
1
A: Deoxyribodipyrimidine photo-lyase
C: Repaired DNA
D: complementary oligonucleotide to the repaired DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,02810
Polymers63,6863
Non-polymers1,3427
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Deoxyribodipyrimidine photo-lyase
E: Repaired DNA
F: complementary oligonucleotide to the repaired DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,8408
Polymers63,6863
Non-polymers1,1545
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.830, 115.040, 167.710
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
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: 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 Repaired DNA


Mass: 4256.767 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain complementary oligonucleotide to the repaired DNA


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

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Non-polymers , 4 types, 568 molecules

#4: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 556 / 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: 2.96 Å3/Da / Density % sol: 58.49 %
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: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jul 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→49.95 Å / Num. obs: 48931 / % possible obs: 99.9 % / Redundancy: 26.53 % / Biso Wilson estimate: 3.19 Å2 / CC1/2: 0.739 / Net I/σ(I): 4.66
Reflection shellResolution: 2.5→2.65 Å / Num. unique obs: 7737 / CC1/2: 0.437 / % possible all: 100

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Processing

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

7yc7


Resolution: 2.5→49.29 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2587 2425 4.96 %
Rwork0.2177 --
obs0.2198 48859 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→49.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6932 1021 165 556 8674
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0058474
X-RAY DIFFRACTIONf_angle_d0.72711721
X-RAY DIFFRACTIONf_dihedral_angle_d20.3653097
X-RAY DIFFRACTIONf_chiral_restr0.0441233
X-RAY DIFFRACTIONf_plane_restr0.0171315
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.550.28061530.24312684X-RAY DIFFRACTION100
2.55-2.610.28291360.25482702X-RAY DIFFRACTION100
2.61-2.670.30361310.26962704X-RAY DIFFRACTION100
2.67-2.730.35061320.2712703X-RAY DIFFRACTION100
2.73-2.810.27681410.23862684X-RAY DIFFRACTION100
2.81-2.890.26541510.21342690X-RAY DIFFRACTION100
2.89-2.980.25751390.20482706X-RAY DIFFRACTION100
2.98-3.090.22361290.19752727X-RAY DIFFRACTION100
3.09-3.210.22591500.20112693X-RAY DIFFRACTION100
3.21-3.360.25611550.19642692X-RAY DIFFRACTION100
3.36-3.540.27681460.21612724X-RAY DIFFRACTION100
3.54-3.760.26331320.21112743X-RAY DIFFRACTION100
3.76-4.050.24911430.20642716X-RAY DIFFRACTION100
4.05-4.460.22431460.17962762X-RAY DIFFRACTION100
4.46-5.10.23811470.19052766X-RAY DIFFRACTION100
5.1-6.420.2281480.21942793X-RAY DIFFRACTION100
6.42-49.290.26071460.24782945X-RAY DIFFRACTION100

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