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- PDB-8z2n: Crystal structure of 5-phosphomethyl-2'-deoxyuridine (5-PmdU) gly... -

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Basic information

Entry
Database: PDB / ID: 8z2n
TitleCrystal structure of 5-phosphomethyl-2'-deoxyuridine (5-PmdU) glycinyltransferase gp46/PUGT from Pseudomonads phage PaMx11 in complex with dsDNA
Components
  • DNA (5'-D(*TP*AP*GP*TP*CP*GP*AP*CP*GP*AP*CP*TP*A)-3')
  • DNA (5'-D(*TP*AP*GP*TP*CP*GP*TP*CP*GP*AP*CP*TP*A)-3')
  • Glycinyltransferase
KeywordsTRANSFERASE/DNA / Pseudomonads phage / DNA / hypermodification / glycinyltransferase / 5-phosphomethyl-2'-deoxyuridine / TRANSFERASE-DNA complex
Function / homology
Function and homology information


symbiont-mediated evasion of host restriction-modification system / transferase activity / symbiont-mediated suppression of host innate immune response / virus-mediated perturbation of host defense response
Similarity search - Function
Amino acid:DNA transferase / Amino acid:DNA transferase
Similarity search - Domain/homology
GLYCINE / DNA / DNA (> 10) / Glycinyltransferase
Similarity search - Component
Biological speciesPseudomonas phage PaMx11 (virus)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsWen, Y. / Guo, W.T. / Wu, B.X.
Funding support1items
OrganizationGrant numberCountry
Not funded
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Glycinyltransferase
C: DNA (5'-D(*TP*AP*GP*TP*CP*GP*TP*CP*GP*AP*CP*TP*A)-3')
D: DNA (5'-D(*TP*AP*GP*TP*CP*GP*AP*CP*GP*AP*CP*TP*A)-3')
CA00: Glycinyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,37711
Polymers74,8624
Non-polymers5157
Water77543
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)57.787, 92.032, 167.644
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 4 through 78 or resid 80 through 291))
d_2ens_1(chain "B" and (resid 4 through 78 or resid 80 through 291))
d_1ens_2(chain "C" and (resid 1 through 6 or resid 8 through 13))
d_2ens_2(chain "D" and (resid 1 through 6 or resid 8...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1ASNASNVALVALCA00D4 - 784 - 78
d_12ens_1GLUGLUTHRTHRCA00D80 - 29180 - 291
d_21ens_1ASNASNVALVALBA4 - 784 - 78
d_22ens_1GLUGLUTHRTHRBA80 - 29180 - 291
d_11ens_2DTDTDADACB1 - 21 - 2
d_21ens_2DTDTDADADC1 - 21 - 2

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(-0.999999474305, -0.00097485117906, 0.00031789224094), (0.00100585001828, -0.992835928016, 0.119481414065), (0.000199138240666, 0.119481671006, 0.992836386641)86.8661581123, 45.5756585407, -3.20830182204
2given(-0.999554928799, 0.0293264681637, -0.00546832503318), (-0.0296993194216, -0.995515286811, 0.0898179500467), (-0.0028097579112, 0.0899403801956, 0.995943187773)86.8293183505, 47.4115244228, -2.00382819588

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Components

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Protein , 1 types, 2 molecules BCA00

#1: Protein Glycinyltransferase / PUGT / Amino acid:DNA transferase / AADT / gp46


Mass: 33459.914 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas phage PaMx11 (virus) / Gene: PaMx11_46 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0S0MVI5

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DNA chain , 2 types, 2 molecules CD

#2: DNA chain DNA (5'-D(*TP*AP*GP*TP*CP*GP*TP*CP*GP*AP*CP*TP*A)-3')


Mass: 3966.597 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*TP*AP*GP*TP*CP*GP*AP*CP*GP*AP*CP*TP*A)-3')


Mass: 3975.611 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 5 types, 50 molecules

#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H5NO2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.98 Å3/Da / Density % sol: 58.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 20% (w/v) PEG 8,000, 0.1M MES/Sodium hydroxide pH 6.0, 0.2M Calcium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 15, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 40612 / % possible obs: 99.9 % / Redundancy: 13.5 % / Biso Wilson estimate: 45.64 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.154 / Rpim(I) all: 0.043 / Rrim(I) all: 0.16 / Net I/σ(I): 12.7
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 13.9 % / Rmerge(I) obs: 1.798 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 5841 / CC1/2: 0.827 / Rpim(I) all: 0.496 / Rrim(I) all: 0.866 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.21rc1_5156refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8Z2M

8z2m


Resolution: 2.3→29 Å / SU ML: 0.3112 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 33.488
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2754 2038 5.04 %
Rwork0.2262 38433 -
obs0.2286 40471 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 57.86 Å2
Refinement stepCycle: LAST / Resolution: 2.3→29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4663 502 28 43 5236
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00975392
X-RAY DIFFRACTIONf_angle_d1.06167420
X-RAY DIFFRACTIONf_chiral_restr0.0532770
X-RAY DIFFRACTIONf_plane_restr0.0169891
X-RAY DIFFRACTIONf_dihedral_angle_d21.03542016
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2BCX-RAY DIFFRACTIONTorsion NCS0.602202379893
ens_2d_2ICA00X-RAY DIFFRACTIONTorsion NCS0.932510809598
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.350.41611250.37982515X-RAY DIFFRACTION99.47
2.35-2.410.41721400.34572523X-RAY DIFFRACTION99.55
2.41-2.480.38291240.32652495X-RAY DIFFRACTION99.51
2.48-2.550.33781370.30852524X-RAY DIFFRACTION99.81
2.55-2.630.38451460.27782543X-RAY DIFFRACTION99.67
2.63-2.730.29861360.27132512X-RAY DIFFRACTION99.89
2.73-2.840.3121210.26372547X-RAY DIFFRACTION99.78
2.84-2.960.3281470.26832534X-RAY DIFFRACTION99.89
2.96-3.120.3181340.2622559X-RAY DIFFRACTION99.89
3.12-3.320.31361390.25592539X-RAY DIFFRACTION99.96
3.32-3.570.28121350.22722589X-RAY DIFFRACTION99.93
3.57-3.930.25911320.21052563X-RAY DIFFRACTION99.78
3.93-4.50.23061390.18412599X-RAY DIFFRACTION100
4.5-5.660.21121440.1792635X-RAY DIFFRACTION100
5.66-290.23281390.18762756X-RAY DIFFRACTION99.59
Refinement TLS params.Method: refined / Origin x: 43.4453268248 Å / Origin y: 24.3929293907 Å / Origin z: 24.4363966068 Å
111213212223313233
T0.407726062522 Å2-0.000650240711813 Å20.0143342247333 Å2-0.608460111076 Å2-0.0497530215978 Å2--0.354717579781 Å2
L0.237983112279 °20.0258439782952 °20.00339674764894 °2-1.03120390665 °2-0.110026682272 °2--0.252013561854 °2
S-0.0350648351837 Å °-0.0523442464207 Å °0.00243247564155 Å °-0.061167090944 Å °0.0671167459903 Å °-0.0223720517791 Å °-0.0190444265636 Å °0.119306958752 Å °-0.0226229977025 Å °
Refinement TLS groupSelection details: all

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