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- PDB-8z79: Crystal structure of 5-N-alpha-glycinylthymidine (N-alpha-GlyT) F... -

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Basic information

Entry
Database: PDB / ID: 8z79
TitleCrystal structure of 5-N-alpha-glycinylthymidine (N-alpha-GlyT) FAD-dependent lyase gp47/NGTO from Pseudomonas phage PaMx11 in complex with dsDNA
Components
  • DNA (5'-D(*TP*AP*GP*TP*CP*AP*TP*GP*AP*CP*T)-3')
  • Flavin-dependent lyase
KeywordsOXIDOREDUCTASE/DNA / N-alpha-GlyT / hypermodification / DNA / complex / Pseudomonads phage / NGTO / FAD / OXIDOREDUCTASE-DNA complex
Function / homology
Function and homology information


symbiont-mediated evasion of host restriction-modification system / : / lyase activity / symbiont-mediated suppression of host innate immune response
Similarity search - Function
FAD dependent oxidoreductase / FAD dependent oxidoreductase / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / DNA / DNA (> 10) / Flavin-dependent lyase
Similarity search - Component
Biological speciesPseudomonas phage PaMx11 (virus)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 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 19, 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

Downloads & links

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Assembly

Deposited unit
A: Flavin-dependent lyase
B: Flavin-dependent lyase
C: Flavin-dependent lyase
D: Flavin-dependent lyase
E: DNA (5'-D(*TP*AP*GP*TP*CP*AP*TP*GP*AP*CP*T)-3')
F: DNA (5'-D(*TP*AP*GP*TP*CP*AP*TP*GP*AP*CP*T)-3')
G: DNA (5'-D(*TP*AP*GP*TP*CP*AP*TP*GP*AP*CP*T)-3')
H: DNA (5'-D(*TP*AP*GP*TP*CP*AP*TP*GP*AP*CP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,73112
Polymers136,5898
Non-polymers3,1424
Water00
1
A: Flavin-dependent lyase
B: Flavin-dependent lyase
E: DNA (5'-D(*TP*AP*GP*TP*CP*AP*TP*GP*AP*CP*T)-3')
F: DNA (5'-D(*TP*AP*GP*TP*CP*AP*TP*GP*AP*CP*T)-3')
G: DNA (5'-D(*TP*AP*GP*TP*CP*AP*TP*GP*AP*CP*T)-3')
H: DNA (5'-D(*TP*AP*GP*TP*CP*AP*TP*GP*AP*CP*T)-3')
hetero molecules

C: Flavin-dependent lyase
D: Flavin-dependent lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,73112
Polymers136,5898
Non-polymers3,1424
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
Unit cell
Length a, b, c (Å)79.380, 102.770, 89.068
Angle α, β, γ (deg.)90.000, 107.984, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 0 through 64 or (resid 65...
d_2ens_1(chain "B" and (resid 0 through 47 or (resid 48...
d_3ens_1(chain "C" and (resid 0 through 1 or (resid 2...
d_4ens_1(chain "D" and (resid 0 through 1 or (resid 2...
d_1ens_2chain "E"
d_2ens_2chain "F"
d_3ens_2chain "G"
d_4ens_2chain "H"

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_1SERSERTYRTYRAA0 - 1041 - 105
d_12ens_1GLUGLUILEILEAA106 - 285107 - 286
d_13ens_1FADFADFADFADAI1301
d_21ens_1SERSERTYRTYRBB0 - 1041 - 105
d_22ens_1GLUGLUILEILEBB106 - 285107 - 286
d_23ens_1FADFADFADFADBJ1301
d_31ens_1SERSERTYRTYRCC0 - 1041 - 105
d_32ens_1GLUGLUILEILECC106 - 285107 - 286
d_33ens_1FADFADFADFADCK301
d_41ens_1SERSERTYRTYRDD0 - 1041 - 105
d_42ens_1GLUGLUILEILEDD106 - 285107 - 286
d_43ens_1FADFADFADFADDL301
d_11ens_2DTDTDTDTEE11
d_21ens_2DTDTDTDTFF11
d_31ens_2DTDTDTDTGG11
d_41ens_2DTDTDTDTHH11

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(0.999654598742, 0.000862342123378, 0.0262667009781), (-0.00130744038516, 0.999855773592, 0.0169328855994), (-0.0262483106856, -0.0169613791051, 0.999511549611)39.552223554, -2.34833149473, 0.876327299608
2given(-0.990008293819, 0.132850204332, -0.0472694550188), (0.124839917191, 0.981636553582, 0.144238246482), (0.065563505432, 0.136895945453, -0.98841333807)66.4420333019, -7.05784733172, 42.6226830843
3given(-0.99099544164, 0.13299602009, -0.015494943986), (0.130319183388, 0.984613239736, 0.116420267038), (0.0307399591715, 0.113352665502, -0.993079165089)106.099994895, -8.19117198836, 43.5637936492
4given(-0.964273232285, 0.250806542181, 0.0852831278634), (0.26441123925, 0.891480828424, 0.367897579648), (0.01624284635, 0.377303605802, -0.925947168574)97.9582959871, -5.4913161491, -37.4706020899
5given(-0.992216483552, 0.123777068482, -0.0136267048626), (0.123503013109, 0.992154671707, 0.0193936371699), (0.0159202864455, 0.0175597473667, -0.999719060412)133.771285113, -8.27220690913, -40.5074163927
6given(0.997820864239, -0.0400323735011, 0.0524493275609), (0.0380129341504, 0.998517830084, 0.0389507360771), (-0.0539308791603, -0.0368721043003, 0.99786367215)39.7371397873, -3.8794581118, 2.1625758958

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Components

#1: Protein
Flavin-dependent lyase / gp47


Mass: 30799.051 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: The first serine is from tag / Source: (gene. exp.) Pseudomonas phage PaMx11 (virus) / Gene: PaMx11_47 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0S0N8M3
#2: DNA chain
DNA (5'-D(*TP*AP*GP*TP*CP*AP*TP*GP*AP*CP*T)-3')


Mass: 3348.209 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
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: 2.54 Å3/Da / Density % sol: 51.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 20% (w/v) PEG 4,000, 0.1M Sodium citrate/Citric acid pH 5.5, 10% (v/v) 2-propanol

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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: Dec 25, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 2.65→30 Å / Num. obs: 39566 / % possible obs: 99.8 % / Redundancy: 4.7 % / Biso Wilson estimate: 48.06 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.118 / Rpim(I) all: 0.06 / Rrim(I) all: 0.133 / Net I/σ(I): 9.7
Reflection shellResolution: 2.65→2.79 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.779 / Mean I/σ(I) obs: 2 / Num. unique obs: 5746 / CC1/2: 0.785 / Rpim(I) all: 0.383 / Rrim(I) all: 0.872 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.21rc1_5156refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8Z2O

8z2o


Resolution: 2.65→29.76 Å / SU ML: 0.3946 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.9533
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2464 1995 5.05 %
Rwork0.2088 37506 -
obs0.2108 39501 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.14 Å2
Refinement stepCycle: LAST / Resolution: 2.65→29.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8427 888 212 0 9527
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00939859
X-RAY DIFFRACTIONf_angle_d1.263813644
X-RAY DIFFRACTIONf_chiral_restr0.06871519
X-RAY DIFFRACTIONf_plane_restr0.01381572
X-RAY DIFFRACTIONf_dihedral_angle_d19.78823434
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.642768095965
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS0.783014577996
ens_1d_4AAX-RAY DIFFRACTIONTorsion NCS0.615581310221
ens_2d_2EEX-RAY DIFFRACTIONTorsion NCS1.76144555556
ens_2d_3EEX-RAY DIFFRACTIONTorsion NCS1.64758862562
ens_2d_4EEX-RAY DIFFRACTIONTorsion NCS1.42578106107
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.65-2.720.33041550.29622640X-RAY DIFFRACTION99.89
2.72-2.790.30631630.27712654X-RAY DIFFRACTION99.79
2.79-2.870.39181320.2712667X-RAY DIFFRACTION99.86
2.87-2.960.34751260.26332705X-RAY DIFFRACTION100
2.96-3.070.28371250.26052682X-RAY DIFFRACTION99.86
3.07-3.190.30861550.26182649X-RAY DIFFRACTION99.89
3.19-3.340.33731470.24782683X-RAY DIFFRACTION99.79
3.34-3.510.28891490.22482655X-RAY DIFFRACTION99.75
3.51-3.730.25571540.21882668X-RAY DIFFRACTION99.93
3.73-4.020.25271440.20192682X-RAY DIFFRACTION99.96
4.02-4.420.21641340.17662687X-RAY DIFFRACTION99.79
4.42-5.060.16571310.16052700X-RAY DIFFRACTION99.75
5.06-6.370.1971440.18982704X-RAY DIFFRACTION99.62
6.37-29.760.17171360.16242730X-RAY DIFFRACTION98.76
Refinement TLS params.Method: refined / Origin x: 54.0252396694 Å / Origin y: -10.8172361859 Å / Origin z: 17.5906856598 Å
111213212223313233
T0.421206543865 Å2-0.00457710940689 Å20.0170019042879 Å2-0.282374092907 Å20.0111798168402 Å2--0.362802357853 Å2
L0.718410651072 °2-0.0692084792621 °2-0.00297760580229 °2-0.0898028495673 °20.0229841254943 °2--0.144311131537 °2
S-0.0124327877566 Å °0.111540247794 Å °0.131469380912 Å °-0.069558146271 Å °0.0069088849602 Å °-0.0245553800306 Å °0.0398231990268 Å °0.0493999546686 Å °0.00166901831628 Å °
Refinement TLS groupSelection details: all

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