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- PDB-7yp4: Crystal structure of elaiophylin glycosyltransferase in apo-form -

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Basic information

Entry
Database: PDB / ID: 7yp4
TitleCrystal structure of elaiophylin glycosyltransferase in apo-form
ComponentsGlycosyltransferase
KeywordsTRANSFERASE / glycosyltransferase / elaiophylin / GT1
Function / homology
Function and homology information


UDP-glycosyltransferase activity / hexosyltransferase activity / antibiotic biosynthetic process / nucleotide binding
Similarity search - Function
Glycosyltransferase, activator-dependent family / : / Erythromycin biosynthesis protein CIII-like, N-terminal domain / Erythromycin biosynthesis protein CIII-like, central / : / Erythromycin biosynthesis protein CIII-like, C-terminal domain / UDP-glucuronosyl/UDP-glucosyltransferase
Similarity search - Domain/homology
R-1,2-PROPANEDIOL / Glycosyltransferase
Similarity search - Component
Biological speciesStreptomyces sp. SCSIO 01934 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 3.1 Å
AuthorsXu, T. / Liu, Q. / Gan, Q. / Liu, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31170708 China
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2022
Title: Substrate-induced dimerization of elaiophylin glycosyltransferase reveals a novel self-activating form of glycosyltransferase for symmetric glycosylation.
Authors: Xu, T. / Gan, Q. / Liu, Q. / Chen, R. / Zhen, X. / Zhang, C. / Liu, J.
History
DepositionAug 2, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 2, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycosyltransferase
B: Glycosyltransferase
C: Glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,16810
Polymers145,6353
Non-polymers5337
Water46826
1
A: Glycosyltransferase
B: Glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,5468
Polymers97,0902
Non-polymers4576
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4610 Å2
ΔGint14 kcal/mol
Surface area31120 Å2
MethodPISA
2
C: Glycosyltransferase
hetero molecules

C: Glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,2424
Polymers97,0902
Non-polymers1522
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area3490 Å2
ΔGint-3 kcal/mol
Surface area30950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.370, 131.210, 225.290
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number17
Space group name H-MP2122
Components on special symmetry positions
IDModelComponents
11A-614-

HOH

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Components

#1: Protein Glycosyltransferase


Mass: 48544.961 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. SCSIO 01934 (bacteria)
Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: E5L4T5
#2: Chemical
ChemComp-PGR / R-1,2-PROPANEDIOL


Mass: 76.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.38 Å3/Da / Density % sol: 63.59 % / Mosaicity: 0.8 °
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.2
Details: 19% polyethylene glycol 3350, 0.15 M DL-Malic pH 7.2, 18% propylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 8, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 3.1→85.47 Å / Num. obs: 36576 / % possible obs: 99.8 % / Redundancy: 4.2 % / CC1/2: 0.992 / Rmerge(I) obs: 0.14 / Rpim(I) all: 0.078 / Rrim(I) all: 0.161 / Net I/σ(I): 7.7 / Num. measured all: 152755 / Scaling rejects: 60
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
3.1-3.244.30.9631889943870.5340.5291.1021.7100
10.74-85.473.80.034387410170.9970.0190.0418.799.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
SCALA3.3.16data scaling
PDB_EXTRACT3.27data extraction
iMOSFLMdata reduction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 7YP3

7yp3


Resolution: 3.1→65.69 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.894 / SU B: 23.402 / SU ML: 0.385 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.441 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2653 1850 5.1 %RANDOM
Rwork0.2136 ---
obs0.2163 34713 99.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 268.29 Å2 / Biso mean: 86.624 Å2 / Biso min: 17.19 Å2
Baniso -1Baniso -2Baniso -3
1-4.67 Å20 Å2-0 Å2
2---2.68 Å20 Å2
3----1.99 Å2
Refinement stepCycle: final / Resolution: 3.1→65.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9543 0 35 26 9604
Biso mean--83.68 42.34 -
Num. residues----1217
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_mcbond_it8.4918.954858
X-RAY DIFFRACTIONr_mcbond_other8.498.954858
X-RAY DIFFRACTIONr_mcangle_it12.87113.3986055
LS refinement shellResolution: 3.1→3.18 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 122 -
Rwork0.319 2554 -
all-2676 -
obs--99.93 %

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