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- PDB-7vja: class II photolyase MmCPDII semiquinone to fully reduced TR-SFX s... -

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Basic information

Entry
Database: PDB / ID: 7vja
Titleclass II photolyase MmCPDII semiquinone to fully reduced TR-SFX studies (10 ns time-point)
ComponentsDNA photolyase
KeywordsFLAVOPROTEIN / photolyase / electron transport / photoreduction / time-resolved serial crystallography.
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
2,3-DIHYDROXY-1,4-DITHIOBUTANE / FLAVIN-ADENINE DINUCLEOTIDE / Deoxyribodipyrimidine photo-lyase
Similarity search - Component
Biological speciesMethanosarcina mazei Go1 (archaea)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsMaestre-Reyna, M. / Yang, C.-H. / Huang, W.-C. / Nango, E. / Ngura Putu, E.P.G. / Franz-Badur, S. / Wu, W.-J. / Wu, H.-Y. / Wang, P.-H. / Hosokawa, Y. ...Maestre-Reyna, M. / Yang, C.-H. / Huang, W.-C. / Nango, E. / Ngura Putu, E.P.G. / Franz-Badur, S. / Wu, W.-J. / Wu, H.-Y. / Wang, P.-H. / Hosokawa, Y. / Saft, M. / Emmerich, H.-J. / Liao, J.-H. / Lee, C.-C. / Huang, K.-F. / Chang, Y.-K. / Weng, J.-H. / Royant, A. / Gad, W. / Pang, A.H. / Chang, C.-W. / Sugahara, M. / Owada, S. / Joti, Y. / Yamashita, A. / Tanaka, R. / Tanaka, T. / Luo, F.J. / Tono, K. / Kiontke, S. / Yamamoto, J. / Iwata, S. / Essen, L.-O. / Bessho, Y. / Tsai, M.-D.
Funding support Taiwan, Japan, 2items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan)AS-KPQ-105-TPP Taiwan
Japan Society for the Promotion of Science (JSPS)16K01942 Japan
CitationJournal: Nat.Chem. / Year: 2022
Title: Serial crystallography captures dynamic control of sequential electron and proton transfer events in a flavoenzyme.
Authors: Maestre-Reyna, M. / Yang, C.H. / Nango, E. / Huang, W.C. / Ngurah Putu, E.P.G. / Wu, W.J. / Wang, P.H. / Franz-Badur, S. / Saft, M. / Emmerich, H.J. / Wu, H.Y. / Lee, C.C. / Huang, K.F. / ...Authors: Maestre-Reyna, M. / Yang, C.H. / Nango, E. / Huang, W.C. / Ngurah Putu, E.P.G. / Wu, W.J. / Wang, P.H. / Franz-Badur, S. / Saft, M. / Emmerich, H.J. / Wu, H.Y. / Lee, C.C. / Huang, K.F. / Chang, Y.K. / Liao, J.H. / Weng, J.H. / Gad, W. / Chang, C.W. / Pang, A.H. / Sugahara, M. / Owada, S. / Hosokawa, Y. / Joti, Y. / Yamashita, A. / Tanaka, R. / Tanaka, T. / Luo, F. / Tono, K. / Hsu, K.C. / Kiontke, S. / Schapiro, I. / Spadaccini, R. / Royant, A. / Yamamoto, J. / Iwata, S. / Essen, L.O. / Bessho, Y. / Tsai, M.D.
History
DepositionSep 28, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 9, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 20, 2022Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed
Revision 1.2Jun 22, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA photolyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,3516
Polymers55,1231
Non-polymers1,2285
Water3,279182
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area220 Å2
ΔGint-18 kcal/mol
Surface area18160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.550, 70.550, 245.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein DNA photolyase / Deoxyribodipyrimidine photo-lyase


Mass: 55123.480 Da / Num. of mol.: 1 / Mutation: M377T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanosarcina mazei Go1 (archaea) / Strain: Go1 / Gene: MM_0852 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: Q8PYK9, deoxyribodipyrimidine photo-lyase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#4: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / Source method: isolated from a natural source / Formula: H2O
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: 2.95 Å3/Da / Density % sol: 58.3 %
Crystal growTemperature: 277 K / Method: microbatch / Details: 0.5-0.65 M Li2SO4 10-15% (W/V) PEG8000

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SACLA / Beamline: BL2 / Wavelength: 1.24 Å
DetectorType: MPCCD / Detector: CCD / Date: Jul 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.24 Å / Relative weight: 1
ReflectionResolution: 2.15→42.6 Å / Num. obs: 34982 / % possible obs: 100 % / Redundancy: 740.6 % / Biso Wilson estimate: 31.96 Å2 / CC1/2: 0.996 / Net I/σ(I): 8.82
Reflection shellResolution: 2.15→2.17 Å / Rmerge(I) obs: 0.55 / Num. unique obs: 1711 / CC1/2: 0.559
Serial crystallography measurementFocal spot size: 1.77 µm2 / Pulse duration: 10 fsec. / Pulse photon energy: 10 keV / XFEL pulse repetition rate: 30 Hz
Serial crystallography sample deliveryDescription: High viscosity injector / Method: injection
Serial crystallography sample delivery injectionCarrier solvent: grease / Filter size: 70 µm / Flow rate: 4.5 µL/min / Injector diameter: 100 µm / Injector nozzle: 100 / Injector temperature: 293 K / Jet diameter: 100 µm / Power by: gas
Serial crystallography data reductionCrystal hits: 27585 / Frames indexed: 19748

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Processing

Software
NameVersionClassification
PHENIX(1.19_4092: ???)refinement
CrystFEL0.6.3data reduction
CrystFEL0.6.3data scaling
REFMAC5.8.0253phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6LMM

6lmm
PDB Unreleased entry


Resolution: 2.15→31.65 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 28.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2197 1680 4.82 %
Rwork0.1979 --
obs0.199 34866 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.15→31.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3537 0 76 182 3795
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0013764
X-RAY DIFFRACTIONf_angle_d0.4645142
X-RAY DIFFRACTIONf_dihedral_angle_d3.131511
X-RAY DIFFRACTIONf_chiral_restr0.039545
X-RAY DIFFRACTIONf_plane_restr0.004655
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.210.39921470.42742709X-RAY DIFFRACTION100
2.21-2.280.42451340.40862694X-RAY DIFFRACTION100
2.28-2.370.4111500.39352692X-RAY DIFFRACTION100
2.37-2.460.41151220.37762714X-RAY DIFFRACTION100
2.46-2.570.43951410.38962723X-RAY DIFFRACTION100
2.57-2.710.32651380.34142735X-RAY DIFFRACTION100
2.71-2.880.30321410.29292725X-RAY DIFFRACTION100
2.88-3.10.28531300.26942775X-RAY DIFFRACTION100
3.1-3.410.21961620.21552738X-RAY DIFFRACTION100
3.41-3.90.16151240.1472815X-RAY DIFFRACTION100
3.9-4.920.11061390.11122844X-RAY DIFFRACTION100
4.92-31.650.11251520.07723022X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 19.3812 Å / Origin y: 25.0021 Å / Origin z: 105.9585 Å
111213212223313233
T0.2942 Å2-0.0039 Å2-0.0069 Å2-0.2784 Å20.0033 Å2--0.2439 Å2
L0.5765 °20.0017 °2-0.0163 °2-0.3072 °2-0.0224 °2--0.4603 °2
S0.0066 Å °0.0096 Å °-0.0047 Å °-0.0098 Å °0.0065 Å °0.0124 Å °0.0032 Å °-0.0128 Å °0.016 Å °
Refinement TLS groupSelection details: all

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