[English] 日本語
Yorodumi
- PDB-4m83: Ensemble refinement of protein crystal structure (2IYF) of macrol... -

+
Open data


ID or keywords:

Loading...

-
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 / response to antibiotic
Similarity search - Function
UDP-glycosyltransferase, MGT-like / 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
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

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

-
Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more