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- PDB-6ep5: Enterococcus faecalis FIC protein in complex with ADP. -

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Basic information

Entry
Database: PDB / ID: 6ep5
TitleEnterococcus faecalis FIC protein in complex with ADP.
ComponentsFic family protein
KeywordsTOXIN
Function / homology
Function and homology information


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
ADENOSINE-5'-DIPHOSPHATE / Fic family protein
Similarity search - Component
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.928 Å
AuthorsVeyron, S. / Cherfils, J.
Funding support France, 1items
OrganizationGrant numberCountry
DIM Malinf France
CitationJournal: Nat Commun / Year: 2019
Title: A Ca2+-regulated deAMPylation switch in human and bacterial FIC proteins.
Authors: Veyron, S. / Oliva, G. / Rolando, M. / Buchrieser, C. / Peyroche, G. / Cherfils, J.
History
DepositionOct 10, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 6, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 13, 2019Group: Data collection / Database references / Structure summary
Category: citation / struct / Item: _citation.title / _struct.title
Revision 1.2Mar 20, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.year
Revision 1.3Jan 17, 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

Downloads & links

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Assembly

Deposited unit
A: Fic family protein
B: Fic family protein
C: Fic family protein
D: Fic family protein
E: Fic family protein
F: Fic family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,38012
Polymers147,8176
Non-polymers2,5636
Water17,330962
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18830 Å2
ΔGint-42 kcal/mol
Surface area48640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.836, 87.836, 364.936
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11B-527-

HOH

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Components

#1: Protein
Fic family protein


Mass: 24636.117 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (bacteria) / Gene: D350_01176 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: U6S0Y1
#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 962 / 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: 2.38 Å3/Da / Density % sol: 48.34 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 50mM Tris pH 8.0, 100mM NaCl, 5mM ATPgS, 2M Ammonium sulfate, 0.1M Bis-Tris pH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.976251 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976251 Å / Relative weight: 1
ReflectionResolution: 1.93→47.3 Å / Num. obs: 108913 / % possible obs: 99.9 % / Redundancy: 13 % / CC1/2: 0.998 / Rmerge(I) obs: 0.172 / Rpim(I) all: 0.071 / Net I/σ(I): 10.35
Reflection shellResolution: 1.93→1.96 Å / Redundancy: 12.6 % / Num. unique obs: 5168 / CC1/2: 0.495 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5NUW

5nuw
PDB Unreleased entry


Resolution: 1.928→47.301 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2402 5426 4.99 %
Rwork0.2003 --
obs0.2024 108653 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.928→47.301 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10018 0 162 962 11142
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00710382
X-RAY DIFFRACTIONf_angle_d0.99214009
X-RAY DIFFRACTIONf_dihedral_angle_d16.4026275
X-RAY DIFFRACTIONf_chiral_restr0.0541491
X-RAY DIFFRACTIONf_plane_restr0.0051778
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9283-1.95020.36281770.35273202X-RAY DIFFRACTION94
1.9502-1.97310.37491640.30893388X-RAY DIFFRACTION100
1.9731-1.99720.35641640.28283436X-RAY DIFFRACTION100
1.9972-2.02250.30921900.2683338X-RAY DIFFRACTION100
2.0225-2.04910.29111740.25993415X-RAY DIFFRACTION100
2.0491-2.07720.31811540.25613404X-RAY DIFFRACTION100
2.0772-2.10680.28141830.24333394X-RAY DIFFRACTION100
2.1068-2.13830.32631850.24893422X-RAY DIFFRACTION100
2.1383-2.17170.2871770.2363368X-RAY DIFFRACTION100
2.1717-2.20730.27651590.23613446X-RAY DIFFRACTION100
2.2073-2.24540.2731700.22983372X-RAY DIFFRACTION100
2.2454-2.28620.32881760.25613415X-RAY DIFFRACTION100
2.2862-2.33020.2651720.22193413X-RAY DIFFRACTION100
2.3302-2.37770.26671820.21163429X-RAY DIFFRACTION100
2.3777-2.42940.29831640.2223418X-RAY DIFFRACTION100
2.4294-2.48590.28721980.21813421X-RAY DIFFRACTION100
2.4859-2.54810.25921740.20273411X-RAY DIFFRACTION100
2.5481-2.6170.26441830.20433417X-RAY DIFFRACTION100
2.617-2.6940.251780.19563452X-RAY DIFFRACTION100
2.694-2.78090.25171690.20753443X-RAY DIFFRACTION100
2.7809-2.88030.2331820.22033423X-RAY DIFFRACTION100
2.8803-2.99560.26711930.2133449X-RAY DIFFRACTION100
2.9956-3.13190.24311970.20773470X-RAY DIFFRACTION100
3.1319-3.2970.25531640.21053461X-RAY DIFFRACTION100
3.297-3.50350.21591730.19793525X-RAY DIFFRACTION100
3.5035-3.77390.21711830.17453482X-RAY DIFFRACTION100
3.7739-4.15350.18622110.16143501X-RAY DIFFRACTION100
4.1535-4.75410.16282230.14833494X-RAY DIFFRACTION100
4.7541-5.98770.23211890.17353609X-RAY DIFFRACTION100
5.9877-47.31530.22962180.18013809X-RAY DIFFRACTION100

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