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- PDB-7vj7: SFX structure of archaeal class II CPD photolyase from Methanosar... -

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Basic information

Entry
Database: PDB / ID: 7vj7
TitleSFX structure of archaeal class II CPD photolyase from Methanosarcina mazei in the fully reduced state
ComponentsDNA photolyase
KeywordsFLAVOPROTEIN / Oxidoreductase / redox state / photoreduction
Function / homology
Function and homology information


deoxyribodipyrimidine photo-lyase / deoxyribodipyrimidine photo-lyase activity / nucleotide binding / 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
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: 2.3 Å
AuthorsMaestre-Reyna, M. / Yang, C.-H. / Huang, W.C. / Nango, E. / Gusti-Ngurah-Putu, E.-P. / Franz-Badur, S. / Wu, W.-J. / Wu, H.-Y. / Wang, P.-H. / Liao, J.-H. ...Maestre-Reyna, M. / Yang, C.-H. / Huang, W.C. / Nango, E. / Gusti-Ngurah-Putu, E.-P. / Franz-Badur, S. / Wu, W.-J. / Wu, H.-Y. / Wang, P.-H. / Liao, J.-H. / Lee, C.-C. / Huang, K.-F. / Chang, Y.-K. / Weng, J.-H. / Sugahara, M. / Owada, S. / Joti, Y. / Tanaka, R. / 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
Water1,13563
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2160 Å2
ΔGint-46 kcal/mol
Surface area18100 Å2
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(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.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL / Dithiothreitol


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#4: 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
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 2.77 Å3/Da / Density % sol: 55.65 %
Crystal growTemperature: 277 K / Method: batch mode / pH: 8 / Details: 0.5-0.65 M Li2SO4, 10-15% (W/V) PEG 8000

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SACLA / Beamline: BL2 / Wavelength: 1.7712035 Å
DetectorType: MPCCD / Detector: CCD / Date: Nov 9, 2017 / Details: K/B mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7712035 Å / Relative weight: 1
ReflectionResolution: 2.3→42.6 Å / Num. obs: 28742 / % possible obs: 100 % / Redundancy: 4.648 % / CC1/2: 0.99 / Net I/σ(I): 6.61
Reflection shellResolution: 2.3→2.382 Å / Redundancy: 2.621 % / Mean I/σ(I) obs: 1.61 / Num. unique obs: 2795 / CC1/2: 0.85 / R split: 2.0618 / % possible all: 100
Serial crystallography measurementPulse photon energy: 7 keV
Serial crystallography sample deliveryDescription: LCP extruder / Method: injection
Serial crystallography sample delivery injectionCarrier solvent: grease / Description: LCP extruder / Flow rate: 1.59 µL/min / Injector diameter: 100 µm / Injector temperature: 293 K / Power by: HPLC
Serial crystallography data reductionCrystal hits: 22191 / Frame hits: 22191 / Frames failed index: 9163 / Frames indexed: 13028

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Processing

Software
NameVersionClassification
PHENIX(1.19_4092: ???)refinement
CrystFEL0.6.3data reduction
CrystFEL0.6.3data scaling
PHASER2.8.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6IWX

6iwx
PDB Unreleased entry


Resolution: 2.3→42.6 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2584 1372 4.79 %
Rwork0.2157 --
obs0.2176 28634 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→42.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3525 0 76 63 3664
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023725
X-RAY DIFFRACTIONf_angle_d0.5295084
X-RAY DIFFRACTIONf_dihedral_angle_d4.59501
X-RAY DIFFRACTIONf_chiral_restr0.038538
X-RAY DIFFRACTIONf_plane_restr0.003648
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.380.36281480.34372642X-RAY DIFFRACTION100
2.38-2.480.3121180.32562664X-RAY DIFFRACTION100
2.48-2.590.4061320.34032675X-RAY DIFFRACTION100
2.59-2.730.32481460.30432676X-RAY DIFFRACTION100
2.73-2.90.31821340.27382674X-RAY DIFFRACTION100
2.9-3.120.34191290.27092718X-RAY DIFFRACTION100
3.12-3.440.26361550.22362697X-RAY DIFFRACTION100
3.44-3.930.22851220.18062763X-RAY DIFFRACTION100
3.93-4.950.19271380.16932784X-RAY DIFFRACTION100
4.95-42.60.25731500.20522969X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.02641.12460.29513.1118-0.73553.4003-0.0109-0.256-0.14860.04080.09880.410.0329-1.0108-0.09290.56680.0334-0.05740.80140.00970.53182.917226.6059110.9467
21.21640.4190.70321.5757-0.56682.7574-0.03040.21770.002-0.34360.06670.09330.1303-0.1545-0.01540.6759-0.0297-0.05570.61020.02120.519815.684724.363399.3751
32.313-0.01980.96981.7966-0.81034.038-0.06670.2334-0.0239-0.102-0.0883-0.1748-0.00310.71310.1730.6281-0.00530.00130.71120.00320.503134.520224.3309108.0239
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 133 )
2X-RAY DIFFRACTION2chain 'A' and (resid 134 through 291 )
3X-RAY DIFFRACTION3chain 'A' and (resid 292 through 462 )

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