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- PDB-5jff: E. coli EcFicT mutant G55R in complex with EcFicA -

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Basic information

Entry
Database: PDB / ID: 5jff
TitleE. coli EcFicT mutant G55R in complex with EcFicA
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


AMPylase activity / protein adenylyltransferase / regulation of cell division / 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
TRIS-HYDROXYMETHYL-METHYL-AMMONIUM / Uncharacterized protein YhfG / Probable protein adenylyltransferase Fic
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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: RCSB / 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,80711
Polymers67,4724
Non-polymers3357
Water8,197455
1
A: Probable adenosine monophosphate-protein transferase fic
B: Uncharacterized protein YhfG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9656
Polymers33,7362
Non-polymers2294
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3960 Å2
ΔGint-51 kcal/mol
Surface area11680 Å2
MethodPISA
2
C: Probable adenosine monophosphate-protein transferase fic
D: Uncharacterized protein YhfG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8425
Polymers33,7362
Non-polymers1063
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3660 Å2
ΔGint-49 kcal/mol
Surface area13400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.690, 104.690, 110.520
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPGLUGLUAA10 - 19534 - 219
21ASPASPGLUGLUCC10 - 19534 - 219
12LEULEUHISHISBB4 - 5217 - 65
22LEULEUHISHISDD4 - 5217 - 65

NCS ensembles :
ID
1
2

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Components

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


Mass: 25727.891 Da / Num. of mol.: 2 / Mutation: G55R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
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: 8008.137 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: yhfG, b3362, JW3325 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0ADX5
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-144 / TRIS-HYDROXYMETHYL-METHYL-AMMONIUM


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 455 / 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: 3.1 Å3/Da / Density % sol: 60.5 % / Mosaicity: 0.14 °
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.2 M MgCl2, 0.1 M Tris pH 8.0, 20% (w/v) PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.9999 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 23, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 2→91 Å / Num. obs: 46198 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 10.2 % / Biso Wilson estimate: 31.66 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.096 / Net I/σ(I): 23.61
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2-2.120.7843.43197.8
2.12-2.270.4565.95199.6
2.27-2.450.2968.81100
2.45-2.680.20113.15199.9
2.68-30.12720.361100
3-3.460.06634.651100
3.46-4.240.03659.731100
4.24-5.990.03364.791100
5.990.0289.68199.9

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Processing

Software
NameVersionClassification
XSCALEdata scaling
REFMAC5.8.0131refinement
PDB_EXTRACT3.2data extraction
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SHG

3shg


Resolution: 2→90.66 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.923 / SU B: 3.35 / SU ML: 0.091 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.137 / ESU R Free: 0.126
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1941 2001 4.3 %RANDOM
Rwork0.1621 ---
obs0.1634 44196 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 111.96 Å2 / Biso mean: 31.732 Å2 / Biso min: 14.81 Å2
Baniso -1Baniso -2Baniso -3
1-0.55 Å20.27 Å20 Å2
2--0.55 Å20 Å2
3----1.77 Å2
Refinement stepCycle: final / Resolution: 2→90.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4016 0 14 455 4485
Biso mean--53.4 36.78 -
Num. residues----490
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0194152
X-RAY DIFFRACTIONr_bond_other_d0.0080.023958
X-RAY DIFFRACTIONr_angle_refined_deg1.7691.9515613
X-RAY DIFFRACTIONr_angle_other_deg1.60539044
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.645494
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.45423.584226
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.73915725
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6591539
X-RAY DIFFRACTIONr_chiral_restr0.120.2594
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.024755
X-RAY DIFFRACTIONr_gen_planes_other0.0080.021044
X-RAY DIFFRACTIONr_mcbond_it2.7532.8191979
X-RAY DIFFRACTIONr_mcbond_other2.7462.8161978
X-RAY DIFFRACTIONr_mcangle_it3.8444.1932472
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A216580.13
12C216580.13
21B48720.17
22D48720.17
LS refinement shellResolution: 2.001→2.053 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 151 -
Rwork0.243 3221 -
all-3372 -
obs--98.42 %

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