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- PDB-9ir0: phage HY126 glycosyltransferase with UDP -

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Basic information

Entry
Database: PDB / ID: 9ir0
Titlephage HY126 glycosyltransferase with UDP
ComponentsGlycosyltransferase subfamily 4-like N-terminal domain-containing protein
KeywordsTRANSFERASE / DNA glycosyltransferase
Function / homologyURIDINE-5'-DIPHOSPHATE / Glycosyltransferase subfamily 4-like N-terminal domain-containing protein
Function and homology information
Biological speciesPhage #D (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.46 Å
AuthorsYu, H. / Lianrong, W.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structure of phage HY126 glycosyltransferase protein at 2.46 angstroms resolution
Authors: Yu, H.
History
DepositionJul 13, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 16, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycosyltransferase subfamily 4-like N-terminal domain-containing protein
B: Glycosyltransferase subfamily 4-like N-terminal domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,3044
Polymers83,4962
Non-polymers8082
Water5,873326
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area660 Å2
ΔGint-7 kcal/mol
Surface area16740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.620, 94.970, 152.020
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

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Components

#1: Protein Glycosyltransferase subfamily 4-like N-terminal domain-containing protein


Mass: 41747.824 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phage #D (virus) / Gene: FFEPELFE_00237 / Production host: Escherichia (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A386K5C4
#2: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: UDP*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 326 / Source method: isolated from a natural source / Formula: H2O
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: 3.01 Å3/Da / Density % sol: 59.13 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.2M Ammonium acetate ; 20% w/v polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 30, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.46→50.67 Å / Num. obs: 37398 / % possible obs: 100 % / Redundancy: 12.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.184 / Net I/σ(I): 13.7
Reflection shellResolution: 2.46→2.52 Å / Mean I/σ(I) obs: 1.6 / Num. unique obs: 2711 / CC1/2: 0.642

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XSCALEdata scaling
PHENIXphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.46→44.71 Å / SU ML: 0.3384 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.572
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2169 2000 5.36 %
Rwork0.2034 35331 -
obs0.2041 37331 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.69 Å2
Refinement stepCycle: LAST / Resolution: 2.46→44.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5858 0 50 326 6234
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00836064
X-RAY DIFFRACTIONf_angle_d1.13538252
X-RAY DIFFRACTIONf_chiral_restr0.0555918
X-RAY DIFFRACTIONf_plane_restr0.01511040
X-RAY DIFFRACTIONf_dihedral_angle_d5.9813796
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.46-2.520.36631400.3192477X-RAY DIFFRACTION100
2.52-2.590.31271410.29812481X-RAY DIFFRACTION99.92
2.59-2.670.29041400.27752487X-RAY DIFFRACTION100
2.67-2.750.31551410.26332486X-RAY DIFFRACTION100
2.75-2.850.2871400.25422476X-RAY DIFFRACTION100
2.85-2.960.26791430.25082522X-RAY DIFFRACTION100
2.96-3.10.25231420.25422506X-RAY DIFFRACTION100
3.1-3.260.24461410.24522501X-RAY DIFFRACTION99.96
3.26-3.470.21061430.2162509X-RAY DIFFRACTION100
3.47-3.730.24831420.20692520X-RAY DIFFRACTION100
3.73-4.110.21841440.18452547X-RAY DIFFRACTION100
4.11-4.70.15341450.15822549X-RAY DIFFRACTION99.96
4.7-5.920.17591450.16052578X-RAY DIFFRACTION100
5.93-44.710.1571530.15792692X-RAY DIFFRACTION99.37

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