[English] 日本語
Yorodumi
- PDB-5tzi: Crystal structure of S. aureus TarS 1-349 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5tzi
TitleCrystal structure of S. aureus TarS 1-349
ComponentsGlycosyl transferase
KeywordsTRANSFERASE / Glycosyltransferase / GT-A / Wall teichoic acid
Function / homology
Function and homology information


poly(ribitol-phosphate) beta-N-acetylglucosaminyltransferase / teichoic acid biosynthetic process / glycosyltransferase activity / cell wall organization / response to antibiotic / metal ion binding
Similarity search - Function
TarS beta-glycosyltransferase C-terminal domain 1 / TarS beta-glycosyltransferase C-terminal domain 1 / TarS C-terminal domain 2 / : / Glycosyl transferase TarS linker domain / Glycosyltransferase 2-like / Glycosyl transferase family 2 / Nucleotide-diphospho-sugar transferases
Similarity search - Domain/homology
Poly(ribitol-phosphate) beta-N-acetylglucosaminyltransferase TarS / :
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsWorrall, L.J. / Sobhanifar, S. / King, D.T. / Strynadka, N.C.
CitationJournal: PLoS Pathog. / Year: 2016
Title: Structure and Mechanism of Staphylococcus aureus TarS, the Wall Teichoic Acid beta-glycosyltransferase Involved in Methicillin Resistance.
Authors: Sobhanifar, S. / Worrall, L.J. / King, D.T. / Wasney, G.A. / Baumann, L. / Gale, R.T. / Nosella, M. / Brown, E.D. / Withers, S.G. / Strynadka, N.C.
History
DepositionNov 21, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 4, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.2Mar 6, 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
C: Glycosyl transferase


Theoretical massNumber of molelcules
Total (without water)42,3181
Polymers42,3181
Non-polymers00
Water2,936163
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area15150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.657, 58.656, 86.676
Angle α, β, γ (deg.)90.000, 97.010, 90.000
Int Tables number5
Space group name H-MC121
DetailsMonomer as determined by SEC-MALS

-
Components

#1: Protein Glycosyl transferase


Mass: 42317.750 Da / Num. of mol.: 1 / Fragment: residues 2-350
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria)
Gene: SAMEA2236484_00765, SAMEA2384030_00583, SAMEA2384487_01253, SAMEA2445549_00791, SAMEA2445572_00749, SAMEA2445608_00472, SAMEA2445616_00196, SAMEA2445622_01196, SAMEA2445624_00746, SAMEA2445630_ ...Gene: SAMEA2236484_00765, SAMEA2384030_00583, SAMEA2384487_01253, SAMEA2445549_00791, SAMEA2445572_00749, SAMEA2445608_00472, SAMEA2445616_00196, SAMEA2445622_01196, SAMEA2445624_00746, SAMEA2445630_01744, SAMEA2445663_00417, SAMEA2445672_00193
Production host: Escherichia coli (E. coli)
References: UniProt: A0A181F8T0, UniProt: A0A0H3JPC6*PLUS, Transferases; Glycosyltransferases; Hexosyltransferases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / 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: 3.09 Å3/Da / Density % sol: 60.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5.5
Details: 0.2 mM lithium sulfate, 27% w/v PEG 3350, and 0.1 M Bis-Tris pH 5.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Oct 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→44.98 Å / Num. obs: 27265 / % possible obs: 94.7 % / Redundancy: 3.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.043 / Rrim(I) all: 0.083 / Net I/σ(I): 12.2 / Num. measured all: 100763
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
2.1-2.163.60.7380.756175.5
8.91-44.983.40.0190.999198.4

-
Processing

Software
NameVersionClassification
xia2data reduction
Aimless0.5.15data scaling
PHASERphasing
PHENIX(1.10_2155)refinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→44.976 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.79
RfactorNum. reflection% reflection
Rfree0.2534 1140 5.32 %
Rwork0.2137 --
obs0.2157 21411 97.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 104.75 Å2 / Biso mean: 50.9461 Å2 / Biso min: 15.93 Å2
Refinement stepCycle: final / Resolution: 2.3→44.976 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2738 0 0 163 2901
Biso mean---46.1 -
Num. residues----337
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052792
X-RAY DIFFRACTIONf_angle_d0.6873775
X-RAY DIFFRACTIONf_chiral_restr0.049418
X-RAY DIFFRACTIONf_plane_restr0.005491
X-RAY DIFFRACTIONf_dihedral_angle_d18.3531701
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.40470.30071470.22742525267298
2.4047-2.53150.281430.23512555269898
2.5315-2.69010.33441270.28962386251392
2.6901-2.89770.25721610.23682546270799
2.8977-3.18930.28051500.23252561271199
3.1893-3.65060.26211360.22622501263796
3.6506-4.59870.21561240.18652529265396
4.5987-44.98490.22661520.18622668282099
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)
11.72350.1456-0.24611.24080.18321.4280.14881.1547-0.2941-0.0695-0.0205-0.05490.16360.4164-0.03960.34740.088-0.01330.8759-0.20290.294127.0107112.8641101.7989
21.42990.0240.17710.8963-0.47610.99220.01610.0401-0.01840.0159-0.0334-0.0367-0.05010.01820.01870.226-0.0101-0.01120.1009-0.0560.26957.4634117.5987127.0695
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'C' and (resid 1 through 218 )C1 - 218
2X-RAY DIFFRACTION2chain 'C' and (resid 219 through 348 )C219 - 348

+
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