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- PDB-6lg3: Crystal structure of a bacterial toxin from Mycobacterium tuberculosis -

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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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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


Mass: 18.015 Da / Num. of mol.: 37 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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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

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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

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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

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