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- PDB-25qc: Crystal structure of Pseudomonas phage YuA Pplase2 in complex wit... -

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Basic information

Entry
Database: PDB / ID: 25qc
TitleCrystal structure of Pseudomonas phage YuA Pplase2 in complex with 5hmdU-DNA and glycine
Components
  • Amino acid:DNA transferase domain-containing protein
  • DNA (5'-D(P*CP*GP*AP*TP*(5HU)P*GP*CP*CP*CP*AP*TP*CP*G)-3')
KeywordsTRANSFERASE / Complex. DNA modification / thymine hypermodification
Function / homologyAmino acid:DNA transferase / Amino acid:DNA transferase / GLYCINE / DNA / DNA (> 10) / Amino acid:DNA transferase domain-containing protein
Function and homology information
Biological speciesPseudomonas virus Yua
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsLi, W. / Zhao, S.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32370704 China
CitationJournal: Nucleic Acids Res. / Year: 2026
Title: Discovery and biosynthesis of a novel diaminopropane-modified thymine in phage DNA
Authors: Li, W. / Chen, H. / Ma, H. / Pan, H. / He, P. / Zhao, S.
History
DepositionApr 14, 2026Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 5, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Amino acid:DNA transferase domain-containing protein
B: DNA (5'-D(P*CP*GP*AP*TP*(5HU)P*GP*CP*CP*CP*AP*TP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,19110
Polymers37,5162
Non-polymers6758
Water2,108117
1
A: Amino acid:DNA transferase domain-containing protein
B: DNA (5'-D(P*CP*GP*AP*TP*(5HU)P*GP*CP*CP*CP*AP*TP*CP*G)-3')
hetero molecules

A: Amino acid:DNA transferase domain-containing protein
B: DNA (5'-D(P*CP*GP*AP*TP*(5HU)P*GP*CP*CP*CP*AP*TP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,38220
Polymers75,0314
Non-polymers1,35116
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-x-1,y,-z+1/21
Buried area8170 Å2
ΔGint-40 kcal/mol
Surface area28580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.489, 200.199, 43.419
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein / DNA chain / Sugars , 3 types, 3 molecules AB

#1: Protein Amino acid:DNA transferase domain-containing protein


Mass: 33572.129 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas virus Yua / Gene: gp10 / Production host: Escherichia coli (E. coli) / References: UniProt: A9J505
#2: DNA chain DNA (5'-D(P*CP*GP*AP*TP*(5HU)P*GP*CP*CP*CP*AP*TP*CP*G)-3')


Mass: 3943.561 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Sugar ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 5 types, 124 molecules

#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5NO2 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / 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: 2.27 Å3/Da / Density % sol: 45.89 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1% (w/v) n-Octyl-beta-D-glucoside, 0.1 M Sodium citrate tribasic dihydrate pH 5.5, 22% (w/v) PEG 3,350.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL18U / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 7, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 17910 / % possible obs: 98.9 % / Redundancy: 12.2 % / CC1/2: 0.978 / CC star: 0.994 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.032 / Rrim(I) all: 0.113 / Χ2: 1.004 / Net I/σ(I): 5.1 / Num. measured all: 218365
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.2-2.289.50.84716120.7780.9350.2750.8940.97991.6
2.28-2.3710.60.78817280.8020.9440.2490.8290.9797.3
2.37-2.4811.60.57817830.9310.9820.1760.6050.97299.8
2.48-2.6112.70.4717800.9670.9920.1360.4891.006100
2.61-2.7713.50.36718010.9780.9950.1030.3811.03100
2.77-2.9913.30.24317930.9890.9970.0690.2531.071100
2.99-3.2912.80.1618010.9940.9980.0460.1661.073100
3.29-3.7613.10.09518310.9970.9990.0270.0991.093100
3.76-4.7412.80.06618340.99910.0190.0690.942100
4.74-5011.80.06319470.9910.9980.020.0660.87499.9

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
HKL-3000data scaling
HKL-3000data reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→21.94 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2261 786 4.89 %
Rwork0.1687 --
obs0.1716 16072 89.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→21.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2344 264 43 120 2771
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072796
X-RAY DIFFRACTIONf_angle_d0.9143837
X-RAY DIFFRACTIONf_dihedral_angle_d18.219468
X-RAY DIFFRACTIONf_chiral_restr0.045387
X-RAY DIFFRACTIONf_plane_restr0.008457
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.340.2736910.20961751X-RAY DIFFRACTION63
2.34-2.520.26251160.20152213X-RAY DIFFRACTION79
2.52-2.770.24961270.19932691X-RAY DIFFRACTION96
2.77-3.170.25531400.19482815X-RAY DIFFRACTION100
3.17-3.990.23181510.15642854X-RAY DIFFRACTION100
3.99-21.940.18821610.1442962X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -21.2934 Å / Origin y: -25.9103 Å / Origin z: 8.8823 Å
111213212223313233
T0.1386 Å2-0.0081 Å20.0156 Å2-0.1643 Å20.0278 Å2--0.1788 Å2
L1.0486 °20.1149 °2-0.117 °2-2.4091 °2-0.0632 °2--1.4754 °2
S0.0125 Å °-0.0595 Å °-0.056 Å °0.1126 Å °0.1258 Å °0.042 Å °-0.0096 Å °-0.0748 Å °-0.1286 Å °
Refinement TLS groupSelection details: all

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