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- PDB-7xx4: designed glycosyltransferase -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 7xx4
Titledesigned glycosyltransferase
ComponentsOleandomycin glycosyltransferase
KeywordsTRANSFERASE / glycosyltransferase
Function / homology
Function and homology information


UDP-glycosyltransferase activity / hexosyltransferase activity / antibiotic biosynthetic process
Similarity search - Function
UDP-glycosyltransferase, MGT-like / Erythromycin biosynthesis protein CIII-like, central / Erythromycin biosynthesis protein CIII-like, C-terminal domain / UDP-glycosyltransferase family, conserved site / UDP-glycosyltransferases signature. / UDP-glucuronosyl/UDP-glucosyltransferase
Similarity search - Domain/homology
URIDINE-5'-DIPHOSPHATE-GLUCOSE / Oleandomycin glycosyltransferase
Similarity search - Component
Biological speciesStreptomyces antibioticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.43 Å
AuthorsLu, M. / Wu, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81973214 China
CitationJournal: Microb Biotechnol / Year: 2023
Title: Design of a chimeric glycosyltransferase OleD for the site-specific O-monoglycosylation of 3-hydroxypyridine in nosiheptide.
Authors: Zhao, L. / Xu, Y. / Chen, M. / Wu, L. / Li, M. / Lu, Y. / Lu, M. / Chen, Y. / Wu, X.
History
DepositionMay 28, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 14, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Dec 27, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Oleandomycin glycosyltransferase
B: Oleandomycin glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,6924
Polymers89,5592
Non-polymers1,1332
Water34219
1
A: Oleandomycin glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3462
Polymers44,7801
Non-polymers5661
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1010 Å2
ΔGint-7 kcal/mol
Surface area16360 Å2
MethodPISA
2
B: Oleandomycin glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3462
Polymers44,7801
Non-polymers5661
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1000 Å2
ΔGint-7 kcal/mol
Surface area16200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.716, 92.285, 191.438
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 7 through 219 or resid 221...
21(chain B and (resid 7 through 219 or resid 221 through 399))

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAALAALA(chain A and (resid 7 through 219 or resid 221...AA7 - 21913 - 225
12GLUGLUTRPTRP(chain A and (resid 7 through 219 or resid 221...AA221 - 224227 - 230
13GLNGLNGLNGLN(chain A and (resid 7 through 219 or resid 221...AA225231
14THRTHRALAALA(chain A and (resid 7 through 219 or resid 221...AA5 - 39911 - 405
21ALAALAALAALA(chain B and (resid 7 through 219 or resid 221 through 399))BB7 - 21913 - 225
22GLUGLUALAALA(chain B and (resid 7 through 219 or resid 221 through 399))BB221 - 399227 - 405

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Components

#1: Protein Oleandomycin glycosyltransferase


Mass: 44779.590 Da / Num. of mol.: 2
Mutation: G65K,D67S,A68N,D69P,P70E,A72S,G74P,S75E,T76D,L77Q,L78E,D79S,N80A,V81M,E82G,P83L,D282P,D288A,A294D,R297T,Q298K,D300S,L301A,V303I,A308M,G310S,S311T,Q312M,G314A,A316S,T317N,T319V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces antibioticus (bacteria) / Gene: oleD / Production host: Escherichia coli (E. coli) / References: UniProt: Q3HTL6
#2: Chemical ChemComp-UPG / URIDINE-5'-DIPHOSPHATE-GLUCOSE / URIDINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE ESTER / Uridine diphosphate glucose


Mass: 566.302 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H24N2O17P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 3.36 Å3/Da / Density % sol: 63.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9.5 / Details: PEG 200, PEG 8000, Bis-Tris pronpane / PH range: 9.0-9.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jan 13, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.43→30.954 Å / Num. obs: 294658 / % possible obs: 99.63 % / Redundancy: 6.36 % / Biso Wilson estimate: 68.72 Å2 / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.08626 / Rpim(I) all: 0.03776 / Rrim(I) all: 0.09437 / Net I/σ(I): 11.36
Reflection shellResolution: 2.43→2.486 Å / Rmerge(I) obs: 1.07 / Num. unique obs: 4558 / CC1/2: 0.744 / CC star: 0.924 / Rpim(I) all: 0.4373 / % possible all: 99.91

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2IYA

2iya


Resolution: 2.43→30.37 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / Phase error: 27.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2386 1185 -
Rwork-82446 -
obs-44607 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 142.1 Å2 / Biso min: 47.97 Å2
Refinement stepCycle: final / Resolution: 2.43→30.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6075 0 72 19 6166
Biso mean--78.04 66.51 -
Num. residues----788
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076308
X-RAY DIFFRACTIONf_angle_d1.0498626
X-RAY DIFFRACTIONf_chiral_restr0.056958
X-RAY DIFFRACTIONf_plane_restr0.0081133
X-RAY DIFFRACTIONf_dihedral_angle_d4.883764
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3644X-RAY DIFFRACTION7.349TORSIONAL
12B3644X-RAY DIFFRACTION7.349TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.43-2.54060.35261470.328110345100
2.5406-2.67440.33571470.29481035399
2.6744-2.84190.30831460.26611042599
2.8419-3.06110.29041470.24721034599
3.0611-3.36890.28181500.23641027999
3.3689-3.85550.22521520.20031028598
3.8555-4.85460.19891460.16621018498
4.8546-5.00030.1851500.17131023098
Refinement TLS params.Method: refined / Origin x: -16.5311 Å / Origin y: -45.4786 Å / Origin z: 26.3062 Å
111213212223313233
T0.5721 Å2-0.0409 Å2-0.0414 Å2-0.6676 Å20.0107 Å2--0.5841 Å2
L0.0617 °20.0094 °2-0.2529 °2-0.9213 °2-0.5048 °2--0.3874 °2
S-0.0091 Å °-0.0481 Å °0.0018 Å °-0.185 Å °0.0032 Å °0.0709 Å °0.0874 Å °-0.009 Å °0.0217 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA5 - 399
2X-RAY DIFFRACTION1allB7 - 399
3X-RAY DIFFRACTION1allC1 - 2
4X-RAY DIFFRACTION1allS1 - 19

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