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- PDB-2a6r: Crystal structure of YoeB under PEG condition -

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Basic information

Entry
Database: PDB / ID: 2a6r
TitleCrystal structure of YoeB under PEG 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
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _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
E: Toxin yoeB
F: Toxin yoeB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,4518
Polymers61,4026
Non-polymers492
Water6,341352
1
A: Toxin yoeB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,2582
Polymers10,2341
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Toxin yoeB


Theoretical massNumber of molelcules
Total (without water)10,2341
Polymers10,2341
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Toxin yoeB


Theoretical massNumber of molelcules
Total (without water)10,2341
Polymers10,2341
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Toxin yoeB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,2582
Polymers10,2341
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Toxin yoeB


Theoretical massNumber of molelcules
Total (without water)10,2341
Polymers10,2341
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Toxin yoeB


Theoretical massNumber of molelcules
Total (without water)10,2341
Polymers10,2341
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)163.898, 43.138, 89.367
Angle α, β, γ (deg.)90.00, 118.49, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Toxin yoeB


Mass: 10233.658 Da / Num. of mol.: 6
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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 352 / 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: 2.3 Å3/Da / Density % sol: 45.3 %
Crystal growTemperature: 293.2 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Tris-HCl, MgCl, PEG8000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.2K

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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: 2.05→44.72 Å / Num. all: 34800 / Num. obs: 34757 / % possible obs: 99.58 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 24.9 Å2 / Χ2: 1.199 / Net I/σ(I): 19.99
Reflection shellResolution: 2.05→2.12 Å / % possible obs: 95.1 % / Redundancy: 3.3 % / Num. measured obs: 3270 / Num. unique all: 3270 / Χ2: 1.035 / % possible all: 95.1

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Phasing

Phasing MRCor.coef. Fo:Fc: 0.569 / Packing: 0.623
Highest resolutionLowest resolutionMethodReflection percentσ(F)
Translation4 Å15 Ågeneral99.5 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: 2.05→14.98 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
Rfree0.229 1719 5 %random
Rwork0.196 ---
all0.2 34700 --
obs0.198 34242 98.4 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 55.6874 Å2 / ksol: 0.418214 e/Å3
Displacement parametersBiso max: 89.28 Å2 / Biso mean: 30.43 Å2 / Biso min: 7.77 Å2
Baniso -1Baniso -2Baniso -3
1-2.38 Å20 Å2-1.77 Å2
2---4.11 Å20 Å2
3---1.73 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.16 Å
Luzzati d res high-2.05
Refinement stepCycle: LAST / Resolution: 2.05→14.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4325 0 14 340 4679
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d21.8
X-RAY DIFFRACTIONc_improper_angle_d0.63
X-RAY DIFFRACTIONc_mcbond_it1.5171.5
X-RAY DIFFRACTIONc_mcangle_it2.442
X-RAY DIFFRACTIONc_scbond_it2.2962
X-RAY DIFFRACTIONc_scangle_it3.4942.5
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 (%)
2.05-2.140.2852064.90.22539720.024326417896.6
2.14-2.260.2551954.60.21640310.0184311422698
2.26-2.40.2522355.60.21239990.0164317423498.1
2.4-2.580.2752385.60.20839860.0184304422498.1
2.58-2.840.2382265.30.20240700.0164354429698.7
2.84-3.250.2322054.80.19340890.0164343429498.8
3.25-4.080.2062215.10.17941270.0144371434899.5
4.08-14.980.1961934.30.1942490.0144499444298.7
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3mo6_xplor_par.txtmo6_xplor_par.txt

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