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- PDB-8z2o: Crystal structure of 5-N-alpha-glycinylthymidine (N-alpha-GlyT) F... -

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Basic information

Entry
Database: PDB / ID: 8z2o
TitleCrystal structure of 5-N-alpha-glycinylthymidine (N-alpha-GlyT) FAD-dependent lyase gp47/NGTO from Pseudomonads phage PaMx11
ComponentsFlavin-dependent lyase
KeywordsOXIDOREDUCTASE / DNA hypermodification / phage / 5-N-apha-glycinylthymidine / N-alpha-GlyT / Pseudomonads PaMx11 / FAD
Function / homologysymbiont-mediated evasion of host restriction-modification system / FAD dependent oxidoreductase / FAD dependent oxidoreductase / : / FAD/NAD(P)-binding domain superfamily / lyase activity / symbiont-mediated suppression of host innate immune response / FLAVIN-ADENINE DINUCLEOTIDE / Flavin-dependent lyase
Function and homology information
Biological speciesPseudomonas phage PaMx11 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsWen, Y. / Guo, W.T. / Wu, B.X.
Funding support China, 1items
OrganizationGrant numberCountry
Not funded China
CitationJournal: Nucleic Acids Res. / Year: 2024
Title: Structural insights into the biosynthetic mechanism of N alpha-GlyT and 5-NmdU hypermodifications of DNA.
Authors: Wen, Y. / Guo, W. / Meng, C. / Yang, J. / Xu, S. / Chen, H. / Gan, J. / Wu, B.
History
DepositionApr 13, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 2, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Flavin-dependent lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2267
Polymers30,7421
Non-polymers1,4846
Water1,71195
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.555, 86.555, 146.699
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Flavin-dependent lyase / NGTO / gp47


Mass: 30742.023 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas phage PaMx11 (virus) / Gene: PaMx11_47 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0S0N8M3

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Non-polymers , 5 types, 101 molecules

#2: Chemical ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES


Mass: 207.290 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H17NO3S / Comment: pH buffer*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: 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
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 5.16 Å3/Da / Density % sol: 76.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 1.0 M Potassium/sodium tartrate, 0.1M CHES/Sodium hydroxide pH 9.5, and 0.2M Lithium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97852 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 28939 / % possible obs: 99.9 % / Redundancy: 19.6 % / Biso Wilson estimate: 42.35 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.126 / Rpim(I) all: 0.029 / Rrim(I) all: 0.13 / Net I/σ(I): 21.4
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 18.1 % / Rmerge(I) obs: 1.201 / Mean I/σ(I) obs: 3 / Num. unique obs: 4153 / CC1/2: 0.92 / Rpim(I) all: 0.288 / Rrim(I) all: 1.236 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→29.75 Å / SU ML: 0.2832 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.0325
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2113 1410 4.89 %
Rwork0.1875 27438 -
obs0.1886 28848 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.21 Å2
Refinement stepCycle: LAST / Resolution: 2.3→29.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2118 0 95 95 2308
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00772273
X-RAY DIFFRACTIONf_angle_d0.92293101
X-RAY DIFFRACTIONf_chiral_restr0.0588334
X-RAY DIFFRACTIONf_plane_restr0.0081387
X-RAY DIFFRACTIONf_dihedral_angle_d11.8655335
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.380.33631480.27062665X-RAY DIFFRACTION99.36
2.38-2.480.29871380.26062710X-RAY DIFFRACTION99.72
2.48-2.590.30361310.25872709X-RAY DIFFRACTION99.65
2.59-2.730.27791380.23282699X-RAY DIFFRACTION99.82
2.73-2.90.25721240.22952747X-RAY DIFFRACTION99.83
2.9-3.120.25981550.21782712X-RAY DIFFRACTION99.93
3.12-3.430.23311420.19762733X-RAY DIFFRACTION99.97
3.44-3.930.1871400.17672764X-RAY DIFFRACTION99.93
3.93-4.950.1791300.14112792X-RAY DIFFRACTION100
4.95-29.750.1491640.16122907X-RAY DIFFRACTION99.74
Refinement TLS params.Method: refined / Origin x: 44.6379425299 Å / Origin y: -24.3459548986 Å / Origin z: -18.6487219094 Å
111213212223313233
T0.262924186166 Å20.0448506710596 Å2-0.00415984952367 Å2-0.391760095277 Å2-0.0181815961703 Å2--0.280193275767 Å2
L0.512158931673 °2-0.272054479129 °20.21088552701 °2-1.98149351327 °2-1.49286367409 °2--3.38868904478 °2
S0.0705516334724 Å °-0.0142552661002 Å °-0.0370745802683 Å °-0.111236510965 Å °-0.033925454564 Å °0.195407969887 Å °0.00916349873746 Å °-0.276311105795 Å °-0.0401481017497 Å °
Refinement TLS groupSelection details: all

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