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- PDB-6y8q: AbiEi antitoxin from Streptococcus agalactiae -

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Basic information

Entry
Database: PDB / ID: 6y8q
TitleAbiEi antitoxin from Streptococcus agalactiae
ComponentsAbortive phage infection protein
KeywordsANTITOXIN / DNA-binding / Toxin-Antitoxin systems / AbiE
Function / homologyTranscriptional regulator, AbiEi antitoxin / Transcriptional regulator, AbiEi antitoxin / DNA-binding transcription repressor activity / protein-DNA complex / transcription cis-regulatory region binding / negative regulation of DNA-templated transcription / Abortive phage infection protein / Abortive infection protein AbiGI
Function and homology information
Biological speciesStreptococcus agalactiae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.83 Å
AuthorsBlower, T.R. / Beck, I.N.
CitationJournal: Biochem.J. / Year: 2020
Title: Antitoxin autoregulation of M. tuberculosis toxin-antitoxin expression through negative cooperativity arising from multiple inverted repeat sequences.
Authors: Beck, I.N. / Usher, B. / Hampton, H.G. / Fineran, P.C. / Blower, T.R.
History
DepositionMar 5, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 16, 2020Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Abortive phage infection protein
B: Abortive phage infection protein
C: Abortive phage infection protein
D: Abortive phage infection protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,8139
Polymers91,8824
Non-polymers9315
Water11,836657
1
A: Abortive phage infection protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0932
Polymers22,9701
Non-polymers1221
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Abortive phage infection protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0932
Polymers22,9701
Non-polymers1221
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Abortive phage infection protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3753
Polymers22,9701
Non-polymers4042
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Abortive phage infection protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2532
Polymers22,9701
Non-polymers2821
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.240, 80.850, 122.170
Angle α, β, γ (deg.)102.480, 96.740, 100.470
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein
Abortive phage infection protein


Mass: 22970.385 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus agalactiae (bacteria) / Gene: AX245_08605, F5043_04970 / Plasmid: pET / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A0E1ENP6, UniProt: Q8DZ36*PLUS
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Chemical ChemComp-B3P / 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL


Mass: 282.334 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H26N2O6 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 657 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.53 Å3/Da / Density % sol: 65.17 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 15% PEG 3350, 0.2 M Sodium acetate trihydrate, 0.1 M 1,3-bis(tris(hydroxymethyl)methylamino)propane

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 11, 2019
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.83→42.11 Å / Num. obs: 106618 / % possible obs: 97.4 % / Redundancy: 1.94 % / Biso Wilson estimate: 29.9 Å2 / CC1/2: 0.999 / Net I/σ(I): 10.7
Reflection shellResolution: 1.83→1.86 Å / Num. unique obs: 5213 / CC1/2: 0.471

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Processing

Software
NameVersionClassification
REFMAC7.0.078refinement
PHENIX1.14_3260refinement
Aimlessdata reduction
xia2data processing
SHELXCDphasing
PHASERphasing
RefinementMethod to determine structure: MAD / Resolution: 1.83→42.1 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 21.8
RfactorNum. reflection% reflection
Rfree0.2095 5193 4.87 %
Rwork0.1813 --
obs0.1827 106601 97.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 39.61 Å2
Refinement stepCycle: LAST / Resolution: 1.83→42.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6397 0 62 657 7116
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01136605
X-RAY DIFFRACTIONf_angle_d1.09778924
X-RAY DIFFRACTIONf_chiral_restr0.0592973
X-RAY DIFFRACTIONf_plane_restr0.00721120
X-RAY DIFFRACTIONf_dihedral_angle_d18.48832502
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.83-1.850.3061650.29533321X-RAY DIFFRACTION96.19
1.85-1.870.33721720.27613367X-RAY DIFFRACTION96.4
1.87-1.90.2891870.27063389X-RAY DIFFRACTION96.44
1.9-1.920.2841540.25913358X-RAY DIFFRACTION96.48
1.92-1.940.27281740.253310X-RAY DIFFRACTION96.19
1.94-1.970.27841690.24873345X-RAY DIFFRACTION97.1
1.97-20.26461620.23313424X-RAY DIFFRACTION96.53
2-2.030.24651930.22033331X-RAY DIFFRACTION97.05
2.03-2.060.24841820.21723294X-RAY DIFFRACTION96.56
2.06-2.090.24081640.20283350X-RAY DIFFRACTION96.38
2.09-2.130.2091960.1943460X-RAY DIFFRACTION97.68
2.13-2.170.21572120.19673273X-RAY DIFFRACTION96.91
2.17-2.210.23321720.19773314X-RAY DIFFRACTION96.7
2.21-2.260.21821510.19323445X-RAY DIFFRACTION97.37
2.26-2.310.20721880.18713381X-RAY DIFFRACTION97.3
2.31-2.360.24411720.18383286X-RAY DIFFRACTION96.73
2.36-2.420.25421690.19283447X-RAY DIFFRACTION96.92
2.42-2.480.22021540.18443374X-RAY DIFFRACTION97.81
2.48-2.560.211630.18343420X-RAY DIFFRACTION98.11
2.56-2.640.21161510.17683469X-RAY DIFFRACTION98.08
2.64-2.730.20561960.17723341X-RAY DIFFRACTION98.09
2.73-2.840.19351960.17753448X-RAY DIFFRACTION98.41
2.84-2.970.18731670.17943363X-RAY DIFFRACTION98.58
2.97-3.130.2111690.18033468X-RAY DIFFRACTION97.8
3.13-3.320.20541590.1753355X-RAY DIFFRACTION98.4
3.32-3.580.18272050.16573401X-RAY DIFFRACTION98.39
3.58-3.940.18711500.15573445X-RAY DIFFRACTION98.71
3.94-4.510.18671790.14253414X-RAY DIFFRACTION98.3
4.51-5.680.16461630.16053435X-RAY DIFFRACTION97.53
5.68-42.10.2421590.19983380X-RAY DIFFRACTION97.57

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