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- PDB-7yp6: Crystal structure of elaiophylin glycosyltransferase in complex w... -

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Basic information

Entry
Database: PDB / ID: 7yp6
TitleCrystal structure of elaiophylin glycosyltransferase in complex with UDP
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, central / Protein of unknown function (DUF1205) / UDP-glucuronosyl/UDP-glucosyltransferase
Similarity search - Domain/homology
R-1,2-PROPANEDIOL / URIDINE-5'-DIPHOSPHATE / Glycosyltransferase
Similarity search - Component
Biological speciesStreptomyces sp. SCSIO 01934 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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

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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)147,66121
Polymers145,6353
Non-polymers2,02618
Water2,738152
1
A: Glycosyltransferase
B: Glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,11620
Polymers97,0902
Non-polymers2,02618
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2900 Å2
ΔGint-9 kcal/mol
Surface area31760 Å2
MethodPISA
2
C: Glycosyltransferase

C: Glycosyltransferase


Theoretical massNumber of molelcules
Total (without water)97,0902
Polymers97,0902
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area2520 Å2
ΔGint-14 kcal/mol
Surface area31270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.796, 131.856, 225.173
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-680-

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-UDP / URIDINE-5'-DIPHOSPHATE / Uridine 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: Chemical
ChemComp-PGR / R-1,2-PROPANEDIOL


Mass: 76.094 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C3H8O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 152 / 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: 3.39 Å3/Da / Density % sol: 63.71 % / Mosaicity: 0.7 °
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.2
Details: 21% polyethylene glycol 3350, 0.15 M DL-Malic pH 7.2, 24% propylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9795 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: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.6→65.23 Å / Num. obs: 62124 / % possible obs: 99.9 % / Redundancy: 4 % / CC1/2: 0.996 / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.059 / Rrim(I) all: 0.12 / Net I/σ(I): 8.4 / Num. measured all: 249252 / Scaling rejects: 65
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
2.6-2.674.11.1111844845530.5240.6271.281.3100
11.63-65.233.40.02627277910.9960.0160.0323.898.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
SCALA3.3.16data scaling
PDB_EXTRACT3.27data extraction
DIALSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7YP3
Resolution: 2.6→64.12 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.921 / SU B: 11.59 / SU ML: 0.233 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.389 / ESU R Free: 0.265 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2468 3105 5 %RANDOM
Rwork0.2116 ---
obs0.2134 58994 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 256.45 Å2 / Biso mean: 75.334 Å2 / Biso min: 27.52 Å2
Baniso -1Baniso -2Baniso -3
1-2.55 Å20 Å2-0 Å2
2---2.34 Å20 Å2
3----0.21 Å2
Refinement stepCycle: final / Resolution: 2.6→64.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9434 0 130 152 9716
Biso mean--75.41 49.98 -
Num. residues----1202
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0129810
X-RAY DIFFRACTIONr_bond_other_d0.0010.0168903
X-RAY DIFFRACTIONr_angle_refined_deg1.5291.63513397
X-RAY DIFFRACTIONr_angle_other_deg0.5291.54620678
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.54551192
X-RAY DIFFRACTIONr_dihedral_angle_2_deg16.7571074
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.174101496
X-RAY DIFFRACTIONr_chiral_restr0.0840.21512
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211101
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021920
LS refinement shellResolution: 2.6→2.667 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.368 230 -
Rwork0.348 4312 -
all-4542 -
obs--99.96 %

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