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- PDB-2a6s: Crystal structure of YoeB under isopropanol condition -

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Basic information

Entry
Database: PDB / ID: 2a6s
TitleCrystal structure of YoeB under isopropanol condition
ComponentsToxin yoeB
KeywordsTOXIN / YoeB / YefM / antitoxin / addiction modules / RNase / inhibitor
Function / homology
Function and homology information


global gene silencing by mRNA cleavage / toxin-antitoxin complex / single-species biofilm formation / regulation of growth / mRNA catabolic process / ribosomal small subunit binding / negative regulation of translational initiation / RNA endonuclease activity / RNA endonuclease activity producing 3'-phosphomonoesters, hydrolytic mechanism / response to heat ...global gene silencing by mRNA cleavage / toxin-antitoxin complex / single-species biofilm formation / regulation of growth / mRNA catabolic process / ribosomal small subunit binding / negative regulation of translational initiation / RNA endonuclease activity / RNA endonuclease activity producing 3'-phosphomonoesters, hydrolytic mechanism / response to heat / endonuclease activity / Hydrolases; Acting on ester bonds / regulation of DNA-templated transcription / protein homodimerization activity / RNA binding
Similarity search - Function
Toxin YoeB / YoeB-like toxin of bacterial type II toxin-antitoxin system / RelE-like / YaeB-like fold / Toxin-antitoxin system, RelE/ParE toxin domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ISOPROPYL ALCOHOL / Toxin YoeB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsKamada, K. / Hanaoka, F.
CitationJournal: Mol.Cell / Year: 2005
Title: Conformational Change in the Catalytic Site of the Ribonuclease YoeB Toxin by YefM Antitoxin
Authors: Kamada, K. / Hanaoka, F.
History
DepositionJul 4, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 23, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Oct 25, 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 / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Toxin yoeB
B: Toxin yoeB
C: Toxin yoeB
D: Toxin yoeB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,29510
Polymers40,9354
Non-polymers3616
Water5,657314
1
A: Toxin yoeB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,2942
Polymers10,2341
Non-polymers601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Toxin yoeB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,4144
Polymers10,2341
Non-polymers1803
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Toxin yoeB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,2942
Polymers10,2341
Non-polymers601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Toxin yoeB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,2942
Polymers10,2341
Non-polymers601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)28.974, 60.989, 98.560
Angle α, β, γ (deg.)90.00, 98.03, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Toxin yoeB


Mass: 10233.658 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: yoeB / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P69348
#2: Chemical
ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 314 / 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: 2.1 Å3/Da / Density % sol: 41.3 %
Crystal growTemperature: 277.2 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Tris-HCl, CH3COONH4, isopropanol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.2K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 28, 2004 / Details: Collimating and Focusing mirrors
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.77→48.8 Å / Num. all: 33197 / Num. obs: 33168 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Biso Wilson estimate: 14.8 Å2 / Χ2: 1.339 / Net I/σ(I): 42.01
Reflection shellResolution: 1.77→1.83 Å / % possible obs: 97.5 % / Redundancy: 6.8 % / Num. measured obs: 3248 / Num. unique all: 3248 / Χ2: 0.954 / % possible all: 97.5

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Phasing

Phasing MRCor.coef. Fo:Fc: 0.489 / Packing: 0.624
Highest resolutionLowest resolutionMethodReflection percentσ(F)
Translation4 Å15 Ågeneral99.2 0

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT1.601data extraction
HKL-2000data reduction
CCP4(TRUNCATE)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: extracted from YoeB structure from 2A6Q

2a6q


Resolution: 1.77→19.96 Å / Rfactor Rfree error: 0.006 / Occupancy max: 1 / Occupancy min: 0 / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.223 1649 5 %random
Rwork0.195 ---
all0.197 33154 --
obs0.196 33036 99.5 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 55.633 Å2 / ksol: 0.446303 e/Å3
Displacement parametersBiso max: 55.56 Å2 / Biso mean: 17.15 Å2 / Biso min: 4.72 Å2
Baniso -1Baniso -2Baniso -3
1--0.7 Å20 Å22.16 Å2
2--0.14 Å20 Å2
3---0.56 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.04 Å-0.06 Å
Luzzati d res high-1.77
Refinement stepCycle: LAST / Resolution: 1.77→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2866 0 0 338 3204
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d21.8
X-RAY DIFFRACTIONc_improper_angle_d0.65
X-RAY DIFFRACTIONc_mcbond_it1.4171.5
X-RAY DIFFRACTIONc_mcangle_it2.2932
X-RAY DIFFRACTIONc_scbond_it2.2252
X-RAY DIFFRACTIONc_scangle_it3.4032.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
1.77-1.850.221894.70.19438620.0164123405198.3
1.85-1.950.2442105.10.19139270.0174166413799.3
1.95-2.070.2351884.60.18339380.0174154412699.3
2.07-2.230.191974.80.17739320.0144148412999.5
2.23-2.450.2212225.40.19138780.0154117410099.6
2.45-2.810.2331994.80.20739460.0164154414599.8
2.81-3.540.2332115.10.19739460.0164166415799.8
3.54-19.960.222335.60.20139580.0144227419199.1
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ioh_xplor_par.txtIOH_XPLOR_top.TXT

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