[English] 日本語
Yorodumi
- PDB-7yp3: Crystal structure of elaiophylin glycosyltransferase in complex w... -

+
Open data


ID or keywords:

Loading...

-
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 / nucleotide binding
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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


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


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


Mass: 18.015 Da / Num. of mol.: 959 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
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

-
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

-
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 %

+
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