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- PDB-8z2m: Crystal structure of 5-phosphomethyl-2'-deoxyuridine (5-PmdU) gly... -

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Basic information

Entry
Database: PDB / ID: 8z2m
TitleCrystal structure of 5-phosphomethyl-2'-deoxyuridine (5-PmdU) glycinyltransferase gp46/PUGT from Pseudomonads phage PaMx11
ComponentsGlycinyltransferase
KeywordsTRANSFERASE / DNA hypermodification / phage / 5-PmdU / glycinyltransferase / Pseudomonads PaMx11
Function / homologyAmino acid:DNA transferase / Amino acid:DNA transferase / 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 / Glycinyltransferase
Function and homology information
Biological speciesPseudomonas phage PaMx11 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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: Glycinyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8445
Polymers33,4601
Non-polymers3844
Water2,450136
1
A: Glycinyltransferase
hetero molecules

A: Glycinyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,68810
Polymers66,9202
Non-polymers7698
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_445-x-1,-y-1,z1
Buried area3640 Å2
ΔGint-147 kcal/mol
Surface area23610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.126, 77.126, 86.385
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number172
Space group name H-MP64
Space group name HallP64
Symmetry operation#1: x,y,z
#2: x-y,x,z+2/3
#3: y,-x+y,z+1/3
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: -x,-y,z
Components on special symmetry positions
IDModelComponents
11A-302-

SO4

21A-514-

HOH

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Components

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


Mass: 33459.914 Da / Num. of mol.: 1
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
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.22 Å3/Da / Density % sol: 44.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Sodium chloride, 0.1 M HEPES pH 7.5, 1.6 M Ammonium 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 PILATUS3 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→30 Å / Num. obs: 19819 / % possible obs: 99.9 % / Redundancy: 20.3 % / Biso Wilson estimate: 28.54 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.139 / Rpim(I) all: 0.031 / Rrim(I) all: 0.142 / Net I/σ(I): 20.7
Reflection shellResolution: 2→2.11 Å / Redundancy: 19.9 % / Rmerge(I) obs: 1.218 / Mean I/σ(I) obs: 3 / Num. unique obs: 2883 / CC1/2: 0.823 / Rpim(I) all: 0.278 / Rrim(I) all: 1.249 / % 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 / Resolution: 2→26.42 Å / SU ML: 0.237 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.0834
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1967 962 4.87 %
Rwork0.1716 18792 -
obs0.1729 19754 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.21 Å2
Refinement stepCycle: LAST / Resolution: 2→26.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2305 0 20 136 2461
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00762389
X-RAY DIFFRACTIONf_angle_d0.79473249
X-RAY DIFFRACTIONf_chiral_restr0.0474334
X-RAY DIFFRACTIONf_plane_restr0.0071425
X-RAY DIFFRACTIONf_dihedral_angle_d15.5913864
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.110.28541150.2312704X-RAY DIFFRACTION100
2.11-2.240.29991670.1992634X-RAY DIFFRACTION99.96
2.24-2.410.23741320.20132706X-RAY DIFFRACTION100
2.41-2.650.23131410.19312643X-RAY DIFFRACTION100
2.65-3.040.21481210.18522701X-RAY DIFFRACTION99.96
3.04-3.820.19031320.16612699X-RAY DIFFRACTION100
3.82-26.420.13861540.13682705X-RAY DIFFRACTION99.93
Refinement TLS params.Method: refined / Origin x: -16.8549425603 Å / Origin y: -17.1929871881 Å / Origin z: 7.18844900117 Å
111213212223313233
T0.171068971037 Å2-0.0157522002345 Å20.0233981489707 Å2-0.147020244646 Å20.00274984785203 Å2--0.148923737861 Å2
L2.50467791773 °2-0.483207803676 °21.29732433069 °2-1.60921363013 °2-0.638430103892 °2--2.02485025111 °2
S0.042669088714 Å °0.00453547140863 Å °-0.0774809995794 Å °-0.0105428494232 Å °0.0866083913962 Å °0.164146473848 Å °0.110321420291 Å °-0.228021523068 Å °-0.125209091809 Å °
Refinement TLS groupSelection details: all

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