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

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Basic information

Entry
Database: PDB / ID: 7vjg
Titleclass II photolyase MmCPDII semiquinone to fully reduced TR-SFX studies (1 us 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: 2.1 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 Japan, 2items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan)AS-KPQ-105-TPP Japan
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
Water3,153175
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area210 Å2
ΔGint-19 kcal/mol
Surface area18110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.520, 70.520, 246.180
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.: 175 / 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: 2.78 Å3/Da / Density % sol: 55.69 %
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: Feb 21, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.24 Å / Relative weight: 1
ReflectionResolution: 1.9→33.9 Å / Num. obs: 50255 / % possible obs: 100 % / Redundancy: 597.05 % / CC1/2: 0.9959 / Net I/σ(I): 6.8
Reflection shellResolution: 1.9→1.92 Å / Redundancy: 123.7 % / Mean I/σ(I) obs: 0.76 / Num. unique obs: 2431 / CC1/2: 0.538 / % possible all: 100
Serial crystallography measurementFocal spot size: 1.77 µm2 / Pulse duration: 10 fsec. / Pulse photon energy: 10 keV
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: 26190 / Frames indexed: 22202

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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: 2.1→31.68 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 27.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1994 1786 4.78 %
Rwork0.1857 --
obs0.1863 37351 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→31.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3537 0 76 175 3788
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043776
X-RAY DIFFRACTIONf_angle_d0.5625160
X-RAY DIFFRACTIONf_dihedral_angle_d11.4391334
X-RAY DIFFRACTIONf_chiral_restr0.04546
X-RAY DIFFRACTIONf_plane_restr0.004658
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.160.511210.48532619X-RAY DIFFRACTION97
2.16-2.220.45531410.45662676X-RAY DIFFRACTION100
2.22-2.290.44491380.42422669X-RAY DIFFRACTION100
2.29-2.370.4211500.39682692X-RAY DIFFRACTION100
2.37-2.470.42481180.3782691X-RAY DIFFRACTION100
2.47-2.580.3741370.38022691X-RAY DIFFRACTION100
2.58-2.720.26091430.30512738X-RAY DIFFRACTION100
2.72-2.890.28191350.25652697X-RAY DIFFRACTION100
2.89-3.110.21761320.2222746X-RAY DIFFRACTION100
3.11-3.420.16451580.18072738X-RAY DIFFRACTION100
3.42-3.920.15261240.12742803X-RAY DIFFRACTION100
3.92-4.930.10161380.09472806X-RAY DIFFRACTION100
4.93-31.680.09161510.07292999X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 19.3414 Å / Origin y: 24.9176 Å / Origin z: 105.9579 Å
111213212223313233
T-0.1324 Å20.1066 Å2-0.0077 Å2--0.0058 Å2-0.0122 Å2---0.0446 Å2
L1.8169 °20.2041 °2-0.0794 °2-2.2968 °2-0.0252 °2--2.9458 °2
S-0.2346 Å °0.2828 Å °-0.007 Å °-0.2118 Å °0.2217 Å °0.0902 Å °0.0966 Å °-0.3089 Å °0.0374 Å °
Refinement TLS groupSelection details: all

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