[English] 日本語
Yorodumi
- PDB-6lg3: Crystal structure of a bacterial toxin from Mycobacterium tuberculosis -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6lg3
TitleCrystal structure of a bacterial toxin from Mycobacterium tuberculosis
ComponentsPhiRv1 phage protein
KeywordsTOXIN / bacterial toxin
Function / homologyPhiRv1 phage protein / Probable PhiRv1 phage protein
Function and homology information
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.90057258182 Å
AuthorsZhou, J. / Jiang, Y. / Luo, Z. / Yin, L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China China
CitationJournal: Sci Adv / Year: 2020
Title: Mycobacterial EST12 activates a RACK1-NLRP3-gasdermin D pyroptosis-IL-1 beta immune pathway.
Authors: Qu, Z. / Zhou, J. / Zhou, Y. / Xie, Y. / Jiang, Y. / Wu, J. / Luo, Z. / Liu, G. / Yin, L. / Zhang, X.L.
History
DepositionDec 4, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 4, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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: PhiRv1 phage protein


Theoretical massNumber of molelcules
Total (without water)8,0391
Polymers8,0391
Non-polymers00
Water66737
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4870 Å2
Unit cell
Length a, b, c (Å)26.539, 60.140, 28.121
Angle α, β, γ (deg.)90.000, 107.847, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

#1: Protein PhiRv1 phage protein


Mass: 8038.860 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0T9XTX3, UniProt: O06611*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 2.66 Å3/Da / Density % sol: 53.71 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 6% v/v Tacsimate pH 6.0, 0.1M MES monohydrate pH 6.0, 25% w/v Polyethylene glycol 4000

-
Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.9→19.35 Å / Num. obs: 12018 / % possible obs: 99 % / Redundancy: 1.9 % / Biso Wilson estimate: 33.1999350093 Å2 / Rmerge(I) obs: 0.143 / Net I/σ(I): 5.71
Reflection shellResolution: 1.901→1.969 Å / Rmerge(I) obs: 0.213 / Mean I/σ(I) obs: 2.37 / Num. unique obs: 634

-
Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2N9V

2n9v


Resolution: 1.90057258182→19.342176936 Å / SU ML: 0.207558956701 / Cross valid method: FREE R-VALUE / σ(F): 1.35089351612 / Phase error: 25.2504637423
RfactorNum. reflection% reflection
Rfree0.243715343531 1217 10.1264769512 %
Rwork0.204580059947 --
obs0.208353516868 12018 92.3396081444 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 39.7739305669 Å2
Refinement stepCycle: LAST / Resolution: 1.90057258182→19.342176936 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms563 0 0 37 600
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00485101942181582
X-RAY DIFFRACTIONf_angle_d0.676935499824792
X-RAY DIFFRACTIONf_chiral_restr0.044342616254490
X-RAY DIFFRACTIONf_plane_restr0.00495905706375105
X-RAY DIFFRACTIONf_dihedral_angle_d18.9869712963347
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9006-1.97660.2842386029821130.2756382775341081X-RAY DIFFRACTION84.8011363636
1.9766-2.06650.2647882095371360.2590757443021210X-RAY DIFFRACTION90.5178211163
2.0665-2.17530.2648440123571310.2320606264291198X-RAY DIFFRACTION91.9087136929
2.1753-2.31130.293032416481360.2333912634621180X-RAY DIFFRACTION91.7073170732
2.3113-2.48950.2517439338571460.2331307720661208X-RAY DIFFRACTION93.2506887052
2.4895-2.73940.2657831139511320.2227561353841241X-RAY DIFFRACTION94.0410958904
2.7394-3.13430.2278984203951450.207526330051233X-RAY DIFFRACTION95.5617198336
3.1343-3.94340.2545513174441380.1884564173061250X-RAY DIFFRACTION96.590118302
3.9434-19.34120.2111303790511400.1783064561631200X-RAY DIFFRACTION92.5414364641
Refinement TLS params.Method: refined / Origin x: 17.8878586915 Å / Origin y: 29.682154433 Å / Origin z: -0.393770085368 Å
111213212223313233
T0.243039211418 Å20.0234858941872 Å20.0139375332337 Å2-0.235074042361 Å20.00153216812728 Å2--0.235422654951 Å2
L1.82414957973 °21.03333042765 °21.27430241317 °2-1.88761087482 °21.57759319263 °2--5.40928679324 °2
S-0.000698895167951 Å °0.0692490375863 Å °-0.0067686949376 Å °-0.068995815362 Å °0.0518546178654 Å °-0.0315982092254 Å °-0.0924476657674 Å °0.209982523731 Å °-0.055603095931 Å °
Refinement TLS groupSelection details: all

+
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