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- PDB-5jfz: E. coli EcFicT in complex with EcFicA mutant E28G -

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Basic information

Entry
Database: PDB / ID: 5jfz
TitleE. coli EcFicT in complex with EcFicA mutant E28G
Components
  • Probable adenosine monophosphate-protein transferase fic
  • Uncharacterized protein YhfG
KeywordsTRANSFERASE / FIC domain / fic-1 / Class I Fic protein
Function / homology
Function and homology information


protein adenylyltransferase / regulation of cell division / nucleotidyltransferase activity / ATP binding
Similarity search - Function
FicA antitoxin homologue YhfG / YhfG / Fido-like domain / Fic-like fold / Fido-like domain superfamily / Fic/DOC family / Fido domain / Fido domain profile. / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Uncharacterized protein YhfG / Probable protein adenylyltransferase Fic
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Escherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsStanger, F.V. / Schirmer, T.
CitationJournal: Plos One / Year: 2016
Title: Crystal Structure of the Escherichia coli Fic Toxin-Like Protein in Complex with Its Cognate Antitoxin.
Authors: Stanger, F.V. / Harms, A. / Dehio, C. / Schirmer, T.
History
DepositionApr 19, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 5, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable adenosine monophosphate-protein transferase fic
B: Uncharacterized protein YhfG
C: Probable adenosine monophosphate-protein transferase fic
D: Uncharacterized protein YhfG
E: Probable adenosine monophosphate-protein transferase fic
F: Uncharacterized protein YhfG


Theoretical massNumber of molelcules
Total (without water)100,6916
Polymers100,6916
Non-polymers00
Water2,648147
1
A: Probable adenosine monophosphate-protein transferase fic
B: Uncharacterized protein YhfG


Theoretical massNumber of molelcules
Total (without water)33,5642
Polymers33,5642
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3050 Å2
ΔGint-21 kcal/mol
Surface area10910 Å2
MethodPISA
2
C: Probable adenosine monophosphate-protein transferase fic
D: Uncharacterized protein YhfG


Theoretical massNumber of molelcules
Total (without water)33,5642
Polymers33,5642
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2800 Å2
ΔGint-20 kcal/mol
Surface area11080 Å2
MethodPISA
3
E: Probable adenosine monophosphate-protein transferase fic
F: Uncharacterized protein YhfG


Theoretical massNumber of molelcules
Total (without water)33,5642
Polymers33,5642
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3130 Å2
ΔGint-20 kcal/mol
Surface area11000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.778, 64.402, 87.884
Angle α, β, γ (deg.)90.000, 113.800, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Probable adenosine monophosphate-protein transferase fic / Cell filamentation protein fic


Mass: 25627.748 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: fic, b3361, JW3324 / Plasmid: pRSFDuet1 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P20605, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
#2: Protein Uncharacterized protein YhfG


Mass: 7936.075 Da / Num. of mol.: 3 / Mutation: E28G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: yhfG, b3362, JW3325 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0ADX5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / 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: 2.5 Å3/Da / Density % sol: 50.9 % / Mosaicity: 0.25 °
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 19% PEG 1500 (w/v), 0.1 M MMT (malic acid, MES, Tris) buffer pH 6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 31, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→80.41 Å / Num. obs: 30850 / % possible obs: 98.6 % / Redundancy: 6.2 % / CC1/2: 0.992 / Rmerge(I) obs: 0.176 / Rpim(I) all: 0.076 / Rrim(I) all: 0.193 / Net I/σ(I): 7.2 / Num. measured all: 192193
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.4-2.496.20.6511754728290.7740.2770.712.386.6
8.97-80.415.70.06836656440.9930.030.07416.199.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4.15 Å80.41 Å
Translation4.15 Å80.41 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0071refinement
Aimless0.1.27data scaling
PHASER2.5.1phasing
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5fjj

5fjj


Resolution: 2.4→80.41 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.886 / SU B: 10.147 / SU ML: 0.234 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.484 / ESU R Free: 0.292 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2727 1583 5.1 %RANDOM
Rwork0.2218 ---
obs0.2244 29267 98.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 104.93 Å2 / Biso mean: 32.801 Å2 / Biso min: 12.84 Å2
Baniso -1Baniso -2Baniso -3
1-2.49 Å20 Å20.01 Å2
2---0.44 Å20 Å2
3----1.48 Å2
Refinement stepCycle: final / Resolution: 2.4→80.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5413 0 0 147 5560
Biso mean---29.86 -
Num. residues----686
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0195528
X-RAY DIFFRACTIONr_bond_other_d0.0010.025216
X-RAY DIFFRACTIONr_angle_refined_deg1.5281.9457484
X-RAY DIFFRACTIONr_angle_other_deg0.89311855
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.175677
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.17123.249277
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.91415894
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8041548
X-RAY DIFFRACTIONr_chiral_restr0.0890.2816
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026360
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021398
X-RAY DIFFRACTIONr_mcbond_it2.2973.2032735
X-RAY DIFFRACTIONr_mcbond_other2.2933.2022734
X-RAY DIFFRACTIONr_mcangle_it3.5944.7943403
LS refinement shellResolution: 2.398→2.46 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 89 -
Rwork0.277 1762 -
all-1851 -
obs--80.55 %

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