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- PDB-7yp3: Crystal structure of elaiophylin glycosyltransferase in complex w... -

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Basic information

Entry
Database: PDB / ID: 7yp3
TitleCrystal structure of elaiophylin glycosyltransferase in complex with elaiophylin
ComponentsGlycosyltransferase
KeywordsTRANSFERASE / glycosyltransferase / elaiophylin / GT1
Function / homology
Function and homology information


UDP-glycosyltransferase activity / hexosyltransferase activity / antibiotic biosynthetic process
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
ACETATE ION / Elaiophylin / Glycosyltransferase
Similarity search - Component
Biological speciesStreptomyces sp. SCSIO 01934 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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
D: Glycosyltransferase
E: Glycosyltransferase
F: Glycosyltransferase
G: Glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)346,78137
Polymers339,8157
Non-polymers6,96630
Water17,276959
1
A: Glycosyltransferase
B: Glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,77912
Polymers97,0902
Non-polymers1,68910
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Glycosyltransferase
D: Glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,3517
Polymers97,0902
Non-polymers2,2615
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Glycosyltransferase
hetero molecules

E: Glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,4438
Polymers97,0902
Non-polymers2,3536
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
4
F: Glycosyltransferase
G: Glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,93014
Polymers97,0902
Non-polymers1,84012
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)228.098, 98.134, 176.506
Angle α, β, γ (deg.)90.000, 103.260, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Glycosyltransferase /


Mass: 48544.961 Da / Num. of mol.: 7
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-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-ELO / Elaiophylin / (3~{E},5~{E},7~{S},8~{S},11~{E},13~{E},15~{S},16~{S})-8,16-bis[(2~{S},3~{R},4~{S})-4-[(2~{R},4~{R},5~{R},6~{R})-5-ethyl-6-methyl-4-[(2~{R},4~{S},5~{S},6~{S})-6-methyl-4,5-bis(oxidanyl)oxan-2-yl]oxy-2-oxidanyl-oxan-2-yl]-3-oxidanyl-pentan-2-yl]-7,15-dimethyl-1,9-dioxacyclohexadeca-3,5,11,13-tetraene-2,10-dione


Mass: 1025.266 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C54H88O18 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 959 / 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: 2.84 Å3/Da / Density % sol: 56.64 % / Mosaicity: 0.54 °
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.8
Details: 5% glycerol 3% PEG 3350 1.7M NH4OAC 0.1M Tris pH 7.8 5% Pentaerythritol ethoxylate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97948 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 29, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97948 Å / Relative weight: 1
ReflectionResolution: 2.1→76.69 Å / Num. obs: 217985 / % possible obs: 98.7 % / Redundancy: 3 % / CC1/2: 0.996 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.048 / Rrim(I) all: 0.087 / Net I/σ(I): 8.3 / Num. measured all: 659590 / Scaling rejects: 1157
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
2.1-2.1420.8051912294520.5640.6561.045187
11.5-76.6930.03429914140.9930.0210.03724.298.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
Aimless0.5.12data scaling
PDB_EXTRACT3.27data extraction
DIALSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3D0R

3d0r


Resolution: 2.1→76.01 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.952 / SU B: 6.286 / SU ML: 0.149 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.188 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2169 10987 5 %RANDOM
Rwork0.1882 ---
obs0.1897 206907 98.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 198.49 Å2 / Biso mean: 53.986 Å2 / Biso min: 23.64 Å2
Baniso -1Baniso -2Baniso -3
1--2.3 Å2-0 Å21.75 Å2
2---1.86 Å2-0 Å2
3---3 Å2
Refinement stepCycle: final / Resolution: 2.1→76.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22599 0 482 959 24040
Biso mean--63.92 49.05 -
Num. residues----2868
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01223731
X-RAY DIFFRACTIONr_bond_other_d0.0020.01621540
X-RAY DIFFRACTIONr_angle_refined_deg1.3511.65632468
X-RAY DIFFRACTIONr_angle_other_deg0.4931.5850109
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.91352865
X-RAY DIFFRACTIONr_dihedral_angle_2_deg17.24310183
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.603103633
X-RAY DIFFRACTIONr_chiral_restr0.0640.23708
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0226774
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024619
LS refinement shellResolution: 2.1→2.155 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 739 -
Rwork0.334 13550 -
all-14289 -
obs--88.01 %

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