[English] 日本語
Yorodumi
- PDB-4m7p: Ensemble refinement of protein crystal structure of macrolide gly... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4m7p
TitleEnsemble refinement of protein crystal structure of macrolide glycosyltransferases OleD
ComponentsOleandomycin glycosyltransferase
KeywordsTRANSFERASE / Structural Genomics / Protein Structure Initiative / Enzyme Discovery for Natural Product Biosynthesis / NatPro / PSI-Biology
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 ...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
Oleandomycin glycosyltransferase / Oleandomycin glycosyltransferase
Similarity search - Component
Biological speciesStreptomyces antibioticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.77 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: To be Published
Title: Crystal structure of macrolide glycosyltransferases OleD
Authors: Olmos Jr., J.L. / Wang, F. / Martinez iii, E. / Helmich, K.E. / Singh, S. / Xu, W. / Bingman, C.A. / Thorson, J.S. / Phillips Jr., G.N.
History
DepositionAug 12, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Oleandomycin glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9532
Polymers45,9301
Non-polymers231
Water2,342130
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)124.134, 124.134, 67.636
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Number of models20
Components on special symmetry positions
IDModelComponents
19A-655-

HOH

-
Components

#1: Protein Oleandomycin glycosyltransferase


Mass: 45929.617 Da / Num. of mol.: 1
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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 43.67 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Protein Solution (10-15 mg/ml protein, 25mM Tris pH 7.5 and 150mM NaCl) mixed in a 1:1 ratio with the well solution (45% polyacrylate 2100, sodium salt, 0.1M HEPES pH 6.5) Cryoprotected with ...Details: Protein Solution (10-15 mg/ml protein, 25mM Tris pH 7.5 and 150mM NaCl) mixed in a 1:1 ratio with the well solution (45% polyacrylate 2100, sodium salt, 0.1M HEPES pH 6.5) Cryoprotected with 45% polyacrylate 2100, sodium salt, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.97939 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 1, 2013
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97939 Å / Relative weight: 1
ReflectionResolution: 1.77→50 Å / Num. all: 37890 / Num. obs: 37890 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.6 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 9.7

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIX(phenix.refine: 1.8.2_1309)model building
PHENIX(phenix.ensemble_refinement: dev_1420)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.8.2_1309phasing
RefinementMethod to determine structure: SAD / Resolution: 1.77→42.081 Å / SU ML: 0.16 / σ(F): 1.3 / Phase error: 20.41 / Stereochemistry target values: ML
Details: AUTHOR MADE THE FOLLOWING COMMENTS: THE ABOUT 10 WATER MOLECULES THAT HAVE 0 B-FACTORS WERE GENERATED AUTOMATICALLY BY PHENIX ENSEMBLE REFINEMENT AND CANNOT BE FURTHER REFINED BY PHENIX ...Details: AUTHOR MADE THE FOLLOWING COMMENTS: THE ABOUT 10 WATER MOLECULES THAT HAVE 0 B-FACTORS WERE GENERATED AUTOMATICALLY BY PHENIX ENSEMBLE REFINEMENT AND CANNOT BE FURTHER REFINED BY PHENIX (BECAUSE PHENIX CURRENTLY DO NOT SUPPORT REGULAR REFINEMENT CONTAINING MULTIPLE MODELS).
RfactorNum. reflection% reflectionSelection details
Rfree0.1884 2004 5.29 %Random
Rwork0.1499 ---
all0.152 37890 --
obs0.152 37890 100 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.77→42.081 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3042 0 1 130 3173
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.016
X-RAY DIFFRACTIONf_angle_d1.867
X-RAY DIFFRACTIONf_dihedral_angle_d18.4
X-RAY DIFFRACTIONf_chiral_restr0.103
X-RAY DIFFRACTIONf_plane_restr0.011
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.77-1.81430.30581420.27582562X-RAY DIFFRACTION100
1.8143-1.86330.30391430.22452559X-RAY DIFFRACTION100
1.8633-1.91820.25661420.18662576X-RAY DIFFRACTION100
1.9182-1.98010.23841420.16652564X-RAY DIFFRACTION100
1.9801-2.05090.2221420.15722554X-RAY DIFFRACTION100
2.0509-2.1330.21551460.14892554X-RAY DIFFRACTION100
2.133-2.230.19671430.14182566X-RAY DIFFRACTION100
2.23-2.34760.19961410.14392599X-RAY DIFFRACTION100
2.3476-2.49470.21511420.13932537X-RAY DIFFRACTION100
2.4947-2.68730.19561430.1472570X-RAY DIFFRACTION100
2.6873-2.95760.1681440.14682561X-RAY DIFFRACTION100
2.9576-3.38540.21261470.15162571X-RAY DIFFRACTION100
3.3854-4.26460.15531400.13862553X-RAY DIFFRACTION100
4.2646-42.0930.1681470.14772560X-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