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- PDB-5ixl: Structure of P. vulgaris HigB toxin Y91A variant -

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Basic information

Entry
Database: PDB / ID: 5ixl
TitleStructure of P. vulgaris HigB toxin Y91A variant
ComponentsEndoribonuclease HigB
KeywordsHYDROLASE / bacterial toxins / biofilms / cell metabolism / energy metabolism / microbial pathogenesis / stress response / stringent response / translation control
Function / homology
Function and homology information


plasmid maintenance / RNA catabolic process / translation repressor activity / RNA endonuclease activity / negative regulation of cell growth / ribosome binding / Hydrolases; Acting on ester bonds / negative regulation of translation / negative regulation of cell population proliferation / mRNA binding
Similarity search - Function
Toxin HigB-1 / RelE-like toxin of type II toxin-antitoxin system HigB / RelE-like / YaeB-like fold / Toxin-antitoxin system, RelE/ParE toxin domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Endoribonuclease HigB
Similarity search - Component
Biological speciesProteus vulgaris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsSchureck, M.A. / Repack, A.A. / Miles, S.J. / Marquez, J. / Dunham, C.M.
CitationJournal: Nucleic Acids Res. / Year: 2016
Title: Mechanism of endonuclease cleavage by the HigB toxin.
Authors: Schureck, M.A. / Repack, A. / Miles, S.J. / Marquez, J. / Dunham, C.M.
History
DepositionMar 23, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2016Group: Database references
Revision 1.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Endoribonuclease HigB
B: Endoribonuclease HigB
C: Endoribonuclease HigB
D: Endoribonuclease HigB
E: Endoribonuclease HigB
F: Endoribonuclease HigB
G: Endoribonuclease HigB
H: Endoribonuclease HigB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,39620
Polymers108,9708
Non-polymers42512
Water10,953608
1
A: Endoribonuclease HigB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6572
Polymers13,6211
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Endoribonuclease HigB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7284
Polymers13,6211
Non-polymers1063
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Endoribonuclease HigB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6572
Polymers13,6211
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Endoribonuclease HigB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6923
Polymers13,6211
Non-polymers712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Endoribonuclease HigB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6572
Polymers13,6211
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Endoribonuclease HigB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6572
Polymers13,6211
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: Endoribonuclease HigB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6572
Polymers13,6211
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: Endoribonuclease HigB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6923
Polymers13,6211
Non-polymers712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)113.340, 64.030, 94.080
Angle α, β, γ (deg.)90.00, 98.14, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Endoribonuclease HigB / Host inhibition of growth protein B / Killer protein / Toxin HigB / mRNA interferase HigB


Mass: 13621.312 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Proteus vulgaris (bacteria) / Gene: higB / Plasmid: pBAD/Myc-HisA / Production host: Escherichia coli BW25113 (bacteria)
References: UniProt: Q7A225, Hydrolases; Acting on ester bonds
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 608 / 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: 1.55 Å3/Da / Density % sol: 20.68 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 40% (w/v) polyethylene glycol monomethylether 2,000 and 0.15 M KBr

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Feb 15, 2015
RadiationMonochromator: Cryogenically-cooled Si-220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.55→100 Å / Num. obs: 87109 / % possible obs: 85.7 % / Redundancy: 2.6 % / Net I/σ(I): 12
Reflection shellResolution: 1.55→1.6 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 2.4 / % possible all: 89.9

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Processing

Software
NameVersionClassification
PHENIX1.8.3_1479refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PX8

4px8


Resolution: 1.55→37.004 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.55
RfactorNum. reflection% reflectionSelection details
Rfree0.2152 1700 1.95 %Random selection
Rwork0.1683 ---
obs0.1692 87109 90.03 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.55→37.004 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6202 0 12 608 6822
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0136389
X-RAY DIFFRACTIONf_angle_d1.3338626
X-RAY DIFFRACTIONf_dihedral_angle_d12.882378
X-RAY DIFFRACTIONf_chiral_restr0.065917
X-RAY DIFFRACTIONf_plane_restr0.0061118
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.59560.27441520.21477326X-RAY DIFFRACTION93
1.5956-1.64710.3121460.20727356X-RAY DIFFRACTION93
1.6471-1.7060.24761460.19397325X-RAY DIFFRACTION93
1.706-1.77430.24211440.1787314X-RAY DIFFRACTION93
1.7743-1.8550.23651370.17357285X-RAY DIFFRACTION92
1.855-1.95280.24081420.16747233X-RAY DIFFRACTION92
1.9528-2.07510.19641410.15917171X-RAY DIFFRACTION91
2.0751-2.23530.21091490.15627162X-RAY DIFFRACTION90
2.2353-2.46020.22341390.1617050X-RAY DIFFRACTION89
2.4602-2.81610.22041360.16986966X-RAY DIFFRACTION88
2.8161-3.54760.17861360.16586798X-RAY DIFFRACTION85
3.5476-37.0140.19991320.16156423X-RAY DIFFRACTION79

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