[English] 日本語
Yorodumi
- PDB-6uf3: Crystal structure of B. subtilis TagV -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6uf3
TitleCrystal structure of B. subtilis TagV
ComponentsPolyisoprenyl-teichoic acid--peptidoglycan teichoic acid transferase TagV
KeywordsTRANSFERASE / LytR / CpsA / Psr
Function / homology
Function and homology information


Transferases; Transferring phosphorus-containing groups; Transferases for other substituted phosphate groups / cell wall organization / transferase activity / plasma membrane
Similarity search - Function
LCP protein / Cell envelope-related transcriptional attenuator domain / LytR_cpsA_psr family / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Polyisoprenyl-teichoic acid--peptidoglycan teichoic acid transferase TagV
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsLi, F.K.K. / Strynadka, N.C.J.
Funding support Canada, United States, 2items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Crystallographic analysis ofStaphylococcus aureusLcpA, the primary wall teichoic acid ligase.
Authors: Li, F.K.K. / Rosell, F.I. / Gale, R.T. / Simorre, J.P. / Brown, E.D. / Strynadka, N.C.J.
History
DepositionSep 23, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 29, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Mar 11, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Polyisoprenyl-teichoic acid--peptidoglycan teichoic acid transferase TagV


Theoretical massNumber of molelcules
Total (without water)30,8241
Polymers30,8241
Non-polymers00
Water3,009167
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.994, 66.104, 81.725
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Polyisoprenyl-teichoic acid--peptidoglycan teichoic acid transferase TagV


Mass: 30823.756 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: tagV, yvhJ, BSU35520 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P96499, Transferases; Transferring phosphorus-containing groups; Transferases for other substituted phosphate groups
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / 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: 1.93 Å3/Da / Density % sol: 36.37 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.3 M ammonium nitrate, 17% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.6→36.643 Å / Num. obs: 30022 / % possible obs: 99.82 % / Redundancy: 7.6 % / CC1/2: 1 / Rmerge(I) obs: 0.06274 / Net I/σ(I): 19
Reflection shellResolution: 1.6→1.657 Å / Redundancy: 7.7 % / Rmerge(I) obs: 1.456 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2963 / CC1/2: 0.709

-
Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NXH

3nxh


Resolution: 1.6→36.643 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.61
RfactorNum. reflection% reflection
Rfree0.2288 1500 5 %
Rwork0.2004 --
obs0.2018 29994 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 99.11 Å2 / Biso mean: 36.2288 Å2 / Biso min: 14.38 Å2
Refinement stepCycle: final / Resolution: 1.6→36.643 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1966 0 0 167 2133
Biso mean---42.53 -
Num. residues----254
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.6-1.65170.34731340.32772553100
1.6517-1.71070.35671340.30072549100
1.7107-1.77920.30191340.26922557100
1.7792-1.86020.29381350.24512551100
1.8602-1.95820.24661340.2142555100
1.9582-2.08090.21611350.19852566100
2.0809-2.24150.23271360.19382567100
2.2415-2.46710.23591360.18872596100
2.4671-2.8240.22511380.19382612100
2.824-3.55740.23681380.18112628100
3.5574-36.6430.19081460.1889276099
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)
14.7210.86430.33772.94540.31852.7219-0.04520.05290.246-0.041-0.09270.2739-0.0776-0.23780.1030.12790.01530.02260.1164-0.00950.160425.392244.469427.6437
23.79080.916-1.4732.6279-1.30843.1604-0.10940.4774-0.0426-0.3359-0.0065-0.1995-0.0060.03060.04430.2115-0.0084-0.0020.2282-0.03070.255237.947252.793917.1614
32.61671.75070.5973.240.83031.6762-0.0222-0.0211-0.29210.0441-0.0115-0.16760.06030.04430.04490.13120.02650.02270.15860.00880.183732.726140.81427.944
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 72 through 155 )A72 - 155
2X-RAY DIFFRACTION2chain 'A' and (resid 156 through 262 )A156 - 262
3X-RAY DIFFRACTION3chain 'A' and (resid 263 through 332 )A263 - 332

+
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://pdbjlvh1.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