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- PDB-4m83: Ensemble refinement of protein crystal structure (2IYF) of macrol... -

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Basic information

Entry
Database: PDB / ID: 4m83
TitleEnsemble refinement of protein crystal structure (2IYF) of macrolide glycosyltransferases OleD complexed with UDP and Erythromycin A
ComponentsOleandomycin glycosyltransferase
KeywordsTransferase/Antibiotic / Structural Genomics / Protein Structure Initiative / Enzyme Discovery for Natural Product Biosynthesis / NatPro / OLEANDOMYCIN GLYCOSYLTRANSFERASE / PSI-Biology / Transferase-Antibiotic complex
Function / homology
Function and homology information


UDP-glycosyltransferase activity / hexosyltransferase activity / Transferases; Glycosyltransferases; Hexosyltransferases / antibiotic biosynthetic process / response to antibiotic
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-glucoronosyl and UDP-glucosyl transferase / UDP-glucuronosyl/UDP-glucosyltransferase / Glycogen Phosphorylase B; / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ERYTHROMYCIN A / URIDINE-5'-DIPHOSPHATE / Oleandomycin glycosyltransferase / Oleandomycin glycosyltransferase
Similarity search - Component
Biological speciesStreptomyces antibioticus (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.698 Å
AuthorsWang, F. / Helmich, K.E. / Xu, W. / Singh, S. / Olmos Jr., J.L. / Martinez iii, E. / Bingman, C.A. / Thorson, J.S. / Phillips Jr., G.N. / Enzyme Discovery for Natural Product Biosynthesis (NatPro)
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2007
Title: The crystal structure of two macrolide glycosyltransferases provides a blueprint for host cell antibiotic immunity.
Authors: Bolam, D.N. / Roberts, S. / Proctor, M.R. / Turkenburg, J.P. / Dodson, E.J. / Martinez-Fleites, C. / Yang, M. / Davis, B.G. / Davies, G.J. / Gilbert, H.J.
History
DepositionAug 12, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 0THIS ENTRY 4M83 REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL STRUCTURAL DATA IN R2IYFSF ...THIS ENTRY 4M83 REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL STRUCTURAL DATA IN R2IYFSF DETERMINED BY AUTHORS OF THE PDB ENTRY 2IYF: D.N.BOLAM,S.M.ROBERTS,M.R.PROCTOR,J.P.TURKENBURG,E.J.DODSON,C.MARTINEZ-FLEITES,M.YANG,B.G.DAVIS,G.J.DAVIES,H.J.GILBERT

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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)93,0327
Polymers90,7322
Non-polymers2,3005
Water9,386521
1
A: Oleandomycin glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5043
Polymers45,3661
Non-polymers1,1382
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Oleandomycin glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5284
Polymers45,3661
Non-polymers1,1623
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.718, 65.778, 91.940
Angle α, β, γ (deg.)90.00, 100.42, 90.00
Int Tables number4
Space group name H-MP1211
Number of models20

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Components

#1: Protein Oleandomycin glycosyltransferase


Mass: 45365.973 Da / Num. of mol.: 2
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, UniProt: Q53685*PLUS
#2: Chemical ChemComp-ERY / ERYTHROMYCIN A / Erythromycin


Mass: 733.927 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C37H67NO13 / Comment: antibiotic*YM
#3: 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 / Comment: UDP*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 521 / Source method: isolated from a natural source / Formula: H2O

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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: 2.38 Å3/Da / Density % sol: 48.39 % / Description: AUTHOR USED THE SF DATA FROM ENTRY 2IYF

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
PHENIX(phenix.ensemble_refinement: dev_1420)refinement
RefinementResolution: 1.698→29.034 Å / SU ML: 0.15 / σ(F): 1.34 / Phase error: 19.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2006 1992 2.12 %
Rwork0.1602 --
obs0.161 94017 99.72 %
all-94281 -
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.698→29.034 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5974 0 153 521 6648
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.007
X-RAY DIFFRACTIONf_angle_d1.362
X-RAY DIFFRACTIONf_dihedral_angle_d16.95
X-RAY DIFFRACTIONf_chiral_restr0.087
X-RAY DIFFRACTIONf_plane_restr0.007
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6981-1.74060.2931380.20166405X-RAY DIFFRACTION97
1.7406-1.78760.23341410.1896524X-RAY DIFFRACTION100
1.7876-1.84020.27911430.19166549X-RAY DIFFRACTION100
1.8402-1.89960.25761410.17926529X-RAY DIFFRACTION100
1.8996-1.96750.20941420.15776557X-RAY DIFFRACTION100
1.9675-2.04630.2021430.15016580X-RAY DIFFRACTION100
2.0463-2.13940.20921420.15236567X-RAY DIFFRACTION100
2.1394-2.25210.19941430.14746558X-RAY DIFFRACTION100
2.2521-2.39320.20831410.14616571X-RAY DIFFRACTION100
2.3932-2.57780.19851420.15716596X-RAY DIFFRACTION100
2.5778-2.83710.20751430.16396582X-RAY DIFFRACTION100
2.8371-3.24710.20041440.16746622X-RAY DIFFRACTION100
3.2471-4.08920.20181430.15446646X-RAY DIFFRACTION100
4.0892-29.03810.14951460.1576739X-RAY DIFFRACTION100

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