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- PDB-7yp5: Crystal structure of elaiophylin glycosyltransferase in complex w... -

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Basic information

Entry
Database: PDB / ID: 7yp5
TitleCrystal structure of elaiophylin glycosyltransferase in complex with TDP
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 / THYMIDINE-5'-DIPHOSPHATE / Glycosyltransferase
Similarity search - Component
Biological speciesStreptomyces sp. SCSIO 01934 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,61514
Polymers97,0902
Non-polymers1,52512
Water2,162120
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7240 Å2
ΔGint-3 kcal/mol
Surface area30530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.210, 106.210, 215.600
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Glycosyltransferase


Mass: 48544.961 Da / Num. of mol.: 2
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-TYD / THYMIDINE-5'-DIPHOSPHATE


Mass: 402.188 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N2O11P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-PGR / R-1,2-PROPANEDIOL


Mass: 76.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.13 Å3/Da / Density % sol: 60.72 % / Mosaicity: 1.04 °
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.2
Details: 22% polyethylene glycol 3350, 0.15 M DL-Malic pH 7.2, 25% propylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 8, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.33→95.28 Å / Num. obs: 50754 / % possible obs: 95.1 % / Redundancy: 24.4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.214 / Rpim(I) all: 0.043 / Rrim(I) all: 0.219 / Net I/σ(I): 10.2 / Num. measured all: 1240470 / Scaling rejects: 1540
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
2.33-2.41222.61210485047580.5540.5472.6741.298.3
9.32-95.2824.30.059237199760.9990.0120.062499.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
Aimless0.5.9data scaling
PDB_EXTRACT3.27data extraction
iMOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7YP3

7yp3


Resolution: 2.33→75.21 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.934 / SU B: 8.83 / SU ML: 0.194 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.294 / ESU R Free: 0.234 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2591 2396 4.7 %RANDOM
Rwork0.2154 ---
obs0.2175 48260 94.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 161.05 Å2 / Biso mean: 49.41 Å2 / Biso min: 22.83 Å2
Baniso -1Baniso -2Baniso -3
1--0.82 Å20 Å2-0 Å2
2---0.82 Å2-0 Å2
3---1.63 Å2
Refinement stepCycle: final / Resolution: 2.33→75.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6568 0 96 120 6784
Biso mean--66.24 40.24 -
Num. residues----838
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0126836
X-RAY DIFFRACTIONr_bond_other_d0.0010.0166193
X-RAY DIFFRACTIONr_angle_refined_deg1.3581.6359346
X-RAY DIFFRACTIONr_angle_other_deg0.4541.54514389
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8435836
X-RAY DIFFRACTIONr_dihedral_angle_2_deg19.3331054
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.733101048
X-RAY DIFFRACTIONr_chiral_restr0.0630.21055
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027776
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021336
LS refinement shellResolution: 2.33→2.39 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.369 189 -
Rwork0.37 3610 -
all-3799 -
obs--97.74 %

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