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- PDB-7viy: class II photolyase MmCPDII oxidized to semiquinone TR-SFX studie... -

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Basic information

Entry
Database: PDB / ID: 7viy
Titleclass II photolyase MmCPDII oxidized to semiquinone TR-SFX studies (50 ns time-point)
ComponentsDNA photolyase
KeywordsFLAVOPROTEIN / photolyase / electron transport / photoreduction / time-resolved serial crystallography
Function / homology
Function and homology information


photoreactive repair / deoxyribodipyrimidine photo-lyase / deoxyribodipyrimidine photo-lyase activity / 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
FLAVIN-ADENINE DINUCLEOTIDE / Deoxyribodipyrimidine photo-lyase
Similarity search - Component
Biological speciesMethanosarcina mazei Go1 (archaea)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 2.25 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)56,0053
Polymers55,1231
Non-polymers8822
Water2,378132
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint-18 kcal/mol
Surface area17950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.760, 70.760, 246.870
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(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q8PYK9, deoxyribodipyrimidine photo-lyase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 132 / 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: 2.8 Å3/Da / Density % sol: 56.12 %
Crystal growTemperature: 278 K / Method: batch mode / 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: 1.2398 Å
DetectorType: MPCCD / Detector: CCD / Date: May 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2398 Å / Relative weight: 1
ReflectionResolution: 1.95→35.57 Å / Num. obs: 47026 / % possible obs: 100 % / Redundancy: 805.8 % / CC1/2: 0.997 / Net I/σ(I): 8
Reflection shellResolution: 1.95→1.97 Å / Mean I/σ(I) obs: 0.67 / Num. unique obs: 2278 / CC1/2: 0.39 / % possible all: 100
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 temperature: 293 K / Jet diameter: 100 µm / Power by: gas
Serial crystallography data reductionCrystal hits: 39644

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Processing

Software
NameVersionClassification
PHENIX(1.19_4092: ???)refinement
PDB_EXTRACT3.25data extraction
CrystFEL0.6.3data reduction
CrystFEL0.6.3data scaling
REFMAC5.8.0253phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6LM4

6lm4
PDB Unreleased entry


Resolution: 2.25→35.57 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 33.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2805 1477 5.02 %
Rwork0.2494 --
obs0.2509 29395 95.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.25→35.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3526 0 58 132 3716
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023716
X-RAY DIFFRACTIONf_angle_d0.6065065
X-RAY DIFFRACTIONf_dihedral_angle_d4.158500
X-RAY DIFFRACTIONf_chiral_restr0.061539
X-RAY DIFFRACTIONf_plane_restr0.006648
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.320.49191150.41052485X-RAY DIFFRACTION95
2.32-2.410.42661170.39932496X-RAY DIFFRACTION95
2.41-2.50.38681290.37012501X-RAY DIFFRACTION95
2.5-2.620.44291440.38222469X-RAY DIFFRACTION95
2.62-2.750.41641630.3592460X-RAY DIFFRACTION95
2.75-2.930.37321410.33432506X-RAY DIFFRACTION95
2.93-3.150.32511570.29932497X-RAY DIFFRACTION95
3.15-3.470.27771190.25732526X-RAY DIFFRACTION95
3.47-3.970.19121250.1942599X-RAY DIFFRACTION96
3.97-50.20651330.16572603X-RAY DIFFRACTION95
5-35.570.19351340.18252776X-RAY DIFFRACTION95
Refinement TLS params.Method: refined / Origin x: 19.6021 Å / Origin y: 24.9629 Å / Origin z: 106.4069 Å
111213212223313233
T0.2213 Å20.0022 Å2-0.0025 Å2-0.1988 Å2-0.0026 Å2--0.1549 Å2
L0.9424 °20.1055 °20.2479 °2-0.6715 °2-0.0984 °2--1.0396 °2
S-0.0156 Å °-0.0338 Å °-0.0157 Å °-0.0323 Å °0.0147 Å °0.0255 Å °-0.0091 Å °-0.0245 Å °0.0027 Å °
Refinement TLS groupSelection details: all

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