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- PDB-4hke: Crystal Structure of MoxT of Bacillus anthracis -

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Basic information

Entry
Database: PDB / ID: 4hke
TitleCrystal Structure of MoxT of Bacillus anthracis
ComponentsAddiction module toxin component PemK
KeywordsTOXIN / SH3 barrel / Ribonuclease fold / toxin protein
Function / homology
Function and homology information


endonuclease activity / Hydrolases; Acting on ester bonds / DNA binding
Similarity search - Function
SH3 type barrels. - #110 / mRNA interferase PemK-like / PemK-like, MazF-like toxin of type II toxin-antitoxin system / Plasmid maintenance toxin/Cell growth inhibitor / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
Addiction module toxin component PemK / mRNA interferase
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsVerma, S. / Kumar, S. / Gourinath, S. / Bhatnagar, R.
CitationJournal: J.Biomol.Struct.Dyn. / Year: 2015
Title: Structural basis of Bacillus anthracis MoxXT disruption and the modulation of MoxT ribonuclease activity by rationally designed peptides.
Authors: Verma, S. / Kumar, S. / Gupta, V.P. / Gourinath, S. / Bhatnagar, S. / Bhatnagar, R.
History
DepositionOct 15, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 13, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 2, 2014Group: Database references
Revision 1.2Aug 24, 2022Group: Database references / Derived calculations
Category: citation / database_2 ...citation / database_2 / struct_ref_seq_dif / struct_site
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Addiction module toxin component PemK
B: Addiction module toxin component PemK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2094
Polymers27,0172
Non-polymers1922
Water3,459192
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3080 Å2
ΔGint-39 kcal/mol
Surface area11470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.163, 70.195, 79.650
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Addiction module toxin component PemK / Transcriptional regulator / PemK family


Mass: 13508.647 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Sterne
Gene: BAS0240, BA_0254, GBAA_0254, pemK, PemK family transcriptional regulator
Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q81VF4, UniProt: A0A6H3ADX7*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 192 / 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: 2.23 Å3/Da / Density % sol: 44.92 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 2M Ammonium sulfate, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 1, 2009 / Details: mirrors
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.87→52.63 Å / Num. obs: 19003

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
REFMAC5.6.0117refinement
AUTOMARdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1NE8

1ne8


Resolution: 1.87→22.61 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.935 / SU B: 2.838 / SU ML: 0.086 / Cross valid method: THROUGHOUT / ESU R: 0.155 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.22456 1620 7.9 %RANDOM
Rwork0.1818 ---
all0.26 ---
obs0.18518 19003 99.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.066 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å20 Å20 Å2
2---0.8 Å20 Å2
3---0.93 Å2
Refinement stepCycle: LAST / Resolution: 1.87→22.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1884 0 10 192 2086
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0191918
X-RAY DIFFRACTIONr_angle_refined_deg1.6311.9762596
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4815238
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.2424.76284
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.2815358
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1931512
X-RAY DIFFRACTIONr_chiral_restr0.1160.2316
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211388
LS refinement shellResolution: 1.87→1.916 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 105 -
Rwork0.263 1193 -
obs--94.47 %

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