[English] 日本語
Yorodumi
- PDB-8dvw: Structure of the Campylobacter concisus glycosyltransferase PglA R203Q -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8dvw
TitleStructure of the Campylobacter concisus glycosyltransferase PglA R203Q
ComponentsN, N'-diacetylbacillosaminyl-diphospho-undecaprenol alpha-1,3-N-acetylgalactosaminyltransferase
KeywordsMEMBRANE PROTEIN / glycosyltransferase / UDP-GalNAc
Function / homologyN,N'-diacetylbacillosaminyl-diphospho-undecaprenol alpha-1,3-N-acetylgalactosaminyltransferase / N,N'-diacetylbacillosaminyl-diphospho-undecaprenol alpha-1,3-N-acetylgalactosaminyltransferase activity / Glycosyltransferase Family 4 / Glycosyltransferase subfamily 4-like, N-terminal domain / Glycosyl transferase, family 1 / Glycosyl transferases group 1 / URIDINE-DIPHOSPHATE-N-ACETYLGALACTOSAMINE / N, N'-diacetylbacillosaminyl-diphospho-undecaprenol alpha-1,3-N-acetylgalactosaminyltransferase
Function and homology information
Biological speciesCampylobacter concisus (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å
AuthorsVuksanovic, N. / Clasman, J.R. / Bernstein, H.M. / Imperiali, B. / Allen, K.N.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM039334 United States
CitationJournal: Protein Sci. / Year: 2024
Title: Specificity determinants revealed by the structure of glycosyltransferase Campylobacter concisus PglA.
Authors: Vuksanovic, N. / Clasman, J.R. / Imperiali, B. / Allen, K.N.
History
DepositionJul 30, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: N, N'-diacetylbacillosaminyl-diphospho-undecaprenol alpha-1,3-N-acetylgalactosaminyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6212
Polymers42,0131
Non-polymers6071
Water1,65792
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)94.924, 94.924, 101.064
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

-
Components

#1: Protein N, N'-diacetylbacillosaminyl-diphospho-undecaprenol alpha-1,3-N-acetylgalactosaminyltransferase


Mass: 42013.371 Da / Num. of mol.: 1 / Mutation: R203Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter concisus (Campylobacter) / Strain: ATCC 33237 / Gene: pglA, CCON33237_1464 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A0M4SVA9, N,N'-diacetylbacillosaminyl-diphospho-undecaprenol alpha-1,3-N-acetylgalactosaminyltransferase
#2: Chemical ChemComp-UD2 / URIDINE-DIPHOSPHATE-N-ACETYLGALACTOSAMINE / (2R,3R,4R,5R,6R)-3-(acetylamino)-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl [(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate


Mass: 607.354 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H27N3O17P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / 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: 3.2 Å3/Da / Density % sol: 61.58 %
Crystal growTemperature: 290.15 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 25% PEG 3350, 0.1 M BIS-TRIS pH 5.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 18, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.29→82.21 Å / Num. obs: 23933 / % possible obs: 99 % / Redundancy: 9.8 % / Biso Wilson estimate: 48.18 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.182 / Rpim(I) all: 0.089 / Rrim(I) all: 0.203 / Net I/σ(I): 8.1
Reflection shellResolution: 2.29→2.37 Å / Redundancy: 9.4 % / Num. unique obs: 2115 / CC1/2: 0.47 / % possible all: 89.6

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6EJI

6eji


Resolution: 2.29→43.05 Å / SU ML: 0.2586 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.8131
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2324 1200 5.03 %
Rwork0.2006 22674 -
obs0.2022 23874 98.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.43 Å2
Refinement stepCycle: LAST / Resolution: 2.29→43.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2886 0 39 92 3017
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00512978
X-RAY DIFFRACTIONf_angle_d0.58764015
X-RAY DIFFRACTIONf_chiral_restr0.0454451
X-RAY DIFFRACTIONf_plane_restr0.0041507
X-RAY DIFFRACTIONf_dihedral_angle_d16.23151085
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.29-2.380.33491400.26532250X-RAY DIFFRACTION90.33
2.38-2.490.29571170.24412523X-RAY DIFFRACTION99.96
2.49-2.620.2641250.24912524X-RAY DIFFRACTION100
2.62-2.790.27551450.23532515X-RAY DIFFRACTION99.92
2.79-30.27311230.23322518X-RAY DIFFRACTION99.96
3-3.30.23581450.22422536X-RAY DIFFRACTION99.96
3.3-3.780.2541680.18662522X-RAY DIFFRACTION99.93
3.78-4.760.1658990.17252609X-RAY DIFFRACTION99.96
4.77-43.050.20761380.18652677X-RAY DIFFRACTION99.65
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.2081791617820.1318734136380.1000242712990.123943986794-0.005486596040530.1651109850590.145821950171-0.184935047826-0.03588453723980.12832453218-0.0962242477551-0.0041924297190.01585977208820.1129830766252.45453939612E-50.5227072521070.0200619844792-0.00108831333810.4858465731680.05112617147010.47746689496559.6792584952-19.543450445215.3452202645
20.485713181866-0.0575540789824-0.0614114968850.632257291243-0.2707624190780.7360649196940.05656169104270.0425968939624-0.00464765853301-0.117514251885-0.0298047377760.00510900241279-0.0128465684643-0.006809720546932.47016000757E-60.4855010419680.02214460883420.02739757838630.409703357648-0.006197909330710.44628111418449.8116968327-8.31432868584-0.643085739677
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 2 through 102 )2 - 1021 - 101
22chain 'A' and (resid 103 through 371 )103 - 371102 - 370

+
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