[English] 日本語
Yorodumi
- PDB-6y6g: lipopolysaccharide outer core galactosyltransferase WaaB apo form -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6y6g
Titlelipopolysaccharide outer core galactosyltransferase WaaB apo form
ComponentsLipopolysaccharide 1,6-galactosyltransferase
KeywordsBIOSYNTHETIC PROTEIN / WaaB / lipopolysaccharide / galactosyltransferase / lipopolysaccharide outer core
Function / homologyGlycosyltransferase Family 4 / Glycosyltransferase subfamily 4-like, N-terminal domain / Glycosyl transferase, family 1 / lipopolysaccharide core region biosynthetic process / Glycosyl transferases group 1 / Transferases; Glycosyltransferases; Hexosyltransferases / glycosyltransferase activity / Lipopolysaccharide 1,6-galactosyltransferase
Function and homology information
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.81 Å
AuthorsZhang, Z.Y. / Ashworth, G. / Wang, Z.S. / Zhu, X.F. / Dong, C.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome TrustWT106121MA United Kingdom
CitationJournal: To Be Published
Title: Structural insights into the lipopolysaccharide outer core galactosyltransferase WaaB
Authors: Zhang, Z.Y. / Ashworth, G. / Wang, Z.S. / Zhu, X.F. / Dong, C.J.
History
DepositionFeb 26, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 31, 2021Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Lipopolysaccharide 1,6-galactosyltransferase


Theoretical massNumber of molelcules
Total (without water)40,9431
Polymers40,9431
Non-polymers00
Water5,891327
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area15870 Å2
Unit cell
Length a, b, c (Å)104.270, 104.270, 88.440
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-407-

HOH

-
Components

#1: Protein Lipopolysaccharide 1,6-galactosyltransferase / UDP-D-galactose--(Glucosyl)lipopolysaccharide-alpha-1 / 3-D-galactosyltransferase


Mass: 40943.172 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: WaaB
Source: (gene. exp.) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
Gene: rfaB, waaB, STM3719
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q06994, Transferases; Glycosyltransferases; Hexosyltransferases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 327 / 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: 2.94 Å3/Da / Density % sol: 58.1 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1% tryptone, 1mM sodium azide, 0.05M HEPES pH7.0 and 20% w/v PEG 3350.

-
Data collection

DiffractionMean temperature: 81 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1.823 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Feb 9, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.823 Å / Relative weight: 1
ReflectionResolution: 1.81→67.54 Å / Num. obs: 44277 / % possible obs: 98.5 % / Redundancy: 60.1 % / CC1/2: 1 / Rmerge(I) obs: 0.125 / Net I/σ(I): 29
Reflection shellResolution: 1.81→1.875 Å / Redundancy: 18.2 % / Rmerge(I) obs: 0.863 / Num. unique obs: 3879 / CC1/2: 0.6 / % possible all: 86.2

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
pointlessdata scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 1.81→67.54 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.954 / SU B: 5.65 / SU ML: 0.075 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.146 / ESU R Free: 0.099
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1956 2225 5 %RANDOM
Rwork0.163 ---
obs0.1646 42052 98.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 106.01 Å2 / Biso mean: 30.493 Å2 / Biso min: 16.25 Å2
Baniso -1Baniso -2Baniso -3
1--1.11 Å20 Å20 Å2
2---1.11 Å20 Å2
3---2.21 Å2
Refinement stepCycle: final / Resolution: 1.81→67.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2837 0 0 327 3164
Biso mean---43.96 -
Num. residues----357
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0132912
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172678
X-RAY DIFFRACTIONr_angle_refined_deg1.3111.6323940
X-RAY DIFFRACTIONr_angle_other_deg1.291.5746217
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7075356
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.21622.766141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.0815497
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.6441512
X-RAY DIFFRACTIONr_chiral_restr0.0810.2380
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023234
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02634
X-RAY DIFFRACTIONr_rigid_bond_restr0.54935590
LS refinement shellResolution: 1.81→1.857 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 138 -
Rwork0.317 2660 -
all-2798 -
obs--85.41 %
Refinement TLS params.Method: refined / Origin x: 106.3279 Å / Origin y: 130.3869 Å / Origin z: 91.3015 Å
111213212223313233
T0.0334 Å20.0187 Å2-0.0179 Å2-0.0555 Å2-0.034 Å2--0.025 Å2
L0.5822 °2-0.09 °20.3266 °2-0.0465 °2-0.1336 °2--0.4154 °2
S-0.0759 Å °-0.0937 Å °0.0983 Å °0.0019 Å °0.021 Å °-0.0179 Å °-0.0261 Å °-0.046 Å °0.0549 Å °

+
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