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- PDB-9iqz: phage HY126 glycosyltransferase -

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Basic information

Entry
Database: PDB / ID: 9iqz
Titlephage HY126 glycosyltransferase
ComponentsGlycosyltransferase subfamily 4-like N-terminal domain-containing protein
KeywordsTRANSFERASE / glycosyltransferase
Function / homologyGlycosyltransferase subfamily 4-like N-terminal domain-containing protein
Function and homology information
Biological speciesPhage #D (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.61 Å
AuthorsYu, H.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: structure of protein XAN60436
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
H: Glycosyltransferase subfamily 4-like N-terminal domain-containing protein
A: Glycosyltransferase subfamily 4-like N-terminal domain-containing protein


Theoretical massNumber of molelcules
Total (without water)83,4962
Polymers83,4962
Non-polymers00
Water3,009167
1
H: Glycosyltransferase subfamily 4-like N-terminal domain-containing protein


Theoretical massNumber of molelcules
Total (without water)41,7481
Polymers41,7481
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Glycosyltransferase subfamily 4-like N-terminal domain-containing protein


Theoretical massNumber of molelcules
Total (without water)41,7481
Polymers41,7481
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.120, 82.720, 139.670
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / Source method: isolated from a natural source / Formula: H2O
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: 2.43 Å3/Da / Density % sol: 49.29 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.2M Ammonium chloride; 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: Oct 13, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.61→49.95 Å / Num. obs: 25518 / % possible obs: 99.9 % / Redundancy: 13 % / CC1/2: 0.999 / Rmerge(I) obs: 0.085 / Net I/σ(I): 24.3
Reflection shellResolution: 2.61→2.72 Å / Num. unique obs: 3048 / CC1/2: 0.961

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.61→49.95 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 25.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2479 1250 4.91 %
Rwork0.1958 --
obs0.1984 25467 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.61→49.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5848 0 0 167 6015
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086002
X-RAY DIFFRACTIONf_angle_d1.0258158
X-RAY DIFFRACTIONf_dihedral_angle_d16.0432210
X-RAY DIFFRACTIONf_chiral_restr0.06908
X-RAY DIFFRACTIONf_plane_restr0.0091036
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.61-2.710.2931190.2352655X-RAY DIFFRACTION100
2.71-2.830.29491340.2412639X-RAY DIFFRACTION100
2.83-2.980.34391330.24262638X-RAY DIFFRACTION100
2.98-3.170.30641530.22562667X-RAY DIFFRACTION100
3.17-3.410.27381470.21592652X-RAY DIFFRACTION100
3.41-3.760.25561460.20232691X-RAY DIFFRACTION100
3.76-4.30.25311430.17752691X-RAY DIFFRACTION100
4.3-5.420.19261320.16462747X-RAY DIFFRACTION100
5.42-49.950.20251430.17852837X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 6.4914 Å / Origin y: 0.3513 Å / Origin z: -3.8526 Å
111213212223313233
T0.2979 Å2-0.0062 Å2-0.0004 Å2-0.3556 Å20.0365 Å2--0.3659 Å2
L0.1827 °20.0784 °20.0082 °2-0.4905 °20.3011 °2--0.619 °2
S0.0461 Å °-0.015 Å °0.0982 Å °-0.0077 Å °-0.0441 Å °-0.0426 Å °0.0127 Å °-0.0252 Å °0.0027 Å °
Refinement TLS groupSelection details: all

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