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- PDB-8wt0: The toxin-antitoxin complex Fic-1-AntF is a deAMPylase that regul... -

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Basic information

Entry
Database: PDB / ID: 8wt0
TitleThe toxin-antitoxin complex Fic-1-AntF is a deAMPylase that regulates the activity of DNA gyrase
Components
  • Cell filamentation protein Fic
  • DUF2559 domain-containing protein
KeywordsSTRUCTURAL PROTEIN / Toxin-antitoxin / AMPylation / deAMPylation / Posttranslational Modification / Filamentation / cyclic adenosine monophosphate protein
Function / homology
Function and homology information


protein adenylyltransferase / regulation of cell division / transferase activity
Similarity search - Function
FicA antitoxin homologue YhfG / YhfG / Fido-like domain superfamily / Fic/DOC family / Fido domain / Fido domain profile.
Similarity search - Domain/homology
D(-)-TARTARIC ACID / protein adenylyltransferase / DUF2559 domain-containing protein
Similarity search - Component
Biological speciesPseudomonas (RNA similarity group I)
Pseudomonas bijieensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsChen, F.R. / Guo, L.W. / Lu, C.H. / Jiang, W.J. / Luo, Z.Q. / Liu, J.F. / Zhang, L.Q.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31572045, 32272611, 32260702, 31901870 China
CitationJournal: To Be Published
Title: The toxin-antitoxin complex Fic-1-AntF is a deAMPylase that regulates the activity of DNA gyrase
Authors: Chen, F.R. / Guo, L.W. / Lu, C.H. / Jiang, W.J. / Luo, Z.Q. / Liu, J.F. / Zhang, L.Q.
History
DepositionOct 17, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 23, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cell filamentation protein Fic
B: DUF2559 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1527
Polymers30,5912
Non-polymers5615
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4020 Å2
ΔGint-61 kcal/mol
Surface area10760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.026, 107.026, 113.529
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Cell filamentation protein Fic / fic-1


Mass: 23366.240 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas (RNA similarity group I) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A172JHQ3
#2: Protein DUF2559 domain-containing protein


Mass: 7225.202 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas bijieensis (bacteria) / Gene: GN234_08370 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6N1CBH0

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Non-polymers , 4 types, 5 molecules

#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#4: Chemical ChemComp-TAR / D(-)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationN

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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: 3.07 Å3/Da / Density % sol: 59.91 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / Details: 1.5 M Li2SO4, 0.1M MES pH 5.6, 0.01 M MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.5→48.41 Å / Num. obs: 13820 / % possible obs: 99.65 % / Redundancy: 19.1 % / CC1/2: 1 / Rmerge(I) obs: 0.1042 / Rpim(I) all: 0.02439 / Rrim(I) all: 0.1071 / Net I/σ(I): 23.02
Reflection shellResolution: 2.5→2.589 Å / Rmerge(I) obs: 1.187 / Mean I/σ(I) obs: 3.07 / Num. unique obs: 1324 / CC1/2: 0.967 / Rpim(I) all: 0.2808 / Rrim(I) all: 1.221 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX1.16refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→48.41 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflectionSelection details
Rfree0.2685 --708
Rwork0.2117 ---
obs-13820 99.65 %-
Refinement stepCycle: LAST / Resolution: 2.5→48.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1801 0 34 0 1835

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