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- PDB-6ep2: Enterococcus faecalis FIC protein in complex with ADP and calcium ion. -

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Basic information

Entry
Database: PDB / ID: 6ep2
TitleEnterococcus faecalis FIC protein in complex with ADP and calcium ion.
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: 2.15 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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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
G: Fic family protein
H: Fic family protein
I: Fic family protein
J: Fic family protein
K: Fic family protein
L: Fic family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)301,72248
Polymers295,63312
Non-polymers6,08836
Water26,8421490
1
A: Fic family protein
B: Fic family protein
C: Fic family protein
D: Fic family protein
E: Fic family protein
L: Fic family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,86124
Polymers147,8176
Non-polymers3,04418
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20340 Å2
ΔGint-214 kcal/mol
Surface area48080 Å2
MethodPISA
2
F: Fic family protein
G: Fic family protein
H: Fic family protein
I: Fic family protein
J: Fic family protein
K: Fic family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,86124
Polymers147,8176
Non-polymers3,04418
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20100 Å2
ΔGint-209 kcal/mol
Surface area48500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.311, 125.311, 362.879
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
11L-516-

HOH

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Components

#1: Protein
Fic family protein


Mass: 24636.117 Da / Num. of mol.: 12
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.: 12
Source method: isolated from a genetically manipulated source
Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical...
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1490 / 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: 2.47 Å3/Da / Density % sol: 50.2 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 14.4 % w/v Polyethylene glycol 8,000 20 % v/v Glycerol, 80 mM MES; pH 6.5, 160 mM Calcium acetate, 5mM MgCl2, 5mM ATPgS

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.15→118.45 Å / Num. obs: 157467 / % possible obs: 100 % / Redundancy: 16.9 % / Biso Wilson estimate: 46.23 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.21 / Rpim(I) all: 0.074 / Net I/σ(I): 12.2
Reflection shellResolution: 2.15→2.19 Å / Redundancy: 17.7 % / Rmerge(I) obs: 1.952 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 7730 / CC1/2: 0.69 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHENIX(1.11.1_2575: ???)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5NUW

5nuw
PDB Unreleased entry


Resolution: 2.15→56.041 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 21.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2178 7890 5.02 %RANDOM
Rwork0.1869 ---
obs0.1884 157231 99.95 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.15→56.041 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20292 0 348 1490 22130
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00521039
X-RAY DIFFRACTIONf_angle_d0.94728388
X-RAY DIFFRACTIONf_dihedral_angle_d13.40812708
X-RAY DIFFRACTIONf_chiral_restr0.0553019
X-RAY DIFFRACTIONf_plane_restr0.0053602
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.17440.30362630.25614931X-RAY DIFFRACTION100
2.1744-2.20.28852680.24334895X-RAY DIFFRACTION100
2.2-2.22680.26222550.22674922X-RAY DIFFRACTION100
2.2268-2.2550.2672640.2344891X-RAY DIFFRACTION100
2.255-2.28470.29252620.23374905X-RAY DIFFRACTION100
2.2847-2.3160.27242480.2224951X-RAY DIFFRACTION100
2.316-2.34910.2472480.21424888X-RAY DIFFRACTION100
2.3491-2.38420.26242620.21654927X-RAY DIFFRACTION100
2.3842-2.42140.24242730.21134907X-RAY DIFFRACTION100
2.4214-2.46110.30392590.21564963X-RAY DIFFRACTION100
2.4611-2.50360.24092660.21244898X-RAY DIFFRACTION100
2.5036-2.54910.25932600.21024917X-RAY DIFFRACTION100
2.5491-2.59810.26522310.21324968X-RAY DIFFRACTION100
2.5981-2.65110.24072430.21024955X-RAY DIFFRACTION100
2.6511-2.70880.25392630.20624925X-RAY DIFFRACTION100
2.7088-2.77180.24712610.19884959X-RAY DIFFRACTION100
2.7718-2.84110.26282720.19864946X-RAY DIFFRACTION100
2.8411-2.91790.23792910.19624938X-RAY DIFFRACTION100
2.9179-3.00380.21752740.19174932X-RAY DIFFRACTION100
3.0038-3.10070.22572610.19454957X-RAY DIFFRACTION100
3.1007-3.21150.24262640.20234990X-RAY DIFFRACTION100
3.2115-3.34010.25442710.19594967X-RAY DIFFRACTION100
3.3401-3.49210.21632520.17925012X-RAY DIFFRACTION100
3.4921-3.67620.19092770.16884990X-RAY DIFFRACTION100
3.6762-3.90640.18792480.16855023X-RAY DIFFRACTION100
3.9064-4.2080.1882790.1585040X-RAY DIFFRACTION100
4.208-4.63130.15792590.14935064X-RAY DIFFRACTION100
4.6313-5.3010.19392620.16395096X-RAY DIFFRACTION100
5.301-6.67690.19272910.19435148X-RAY DIFFRACTION100
6.6769-56.05980.1762630.16595436X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -65.4758 Å / Origin y: 31.1656 Å / Origin z: -60.3444 Å
111213212223313233
T0.2033 Å20.0107 Å2-0.0176 Å2-0.1926 Å20.0399 Å2--0.216 Å2
L0.1213 °20.0422 °20.072 °2-0.2215 °20.1662 °2--0.2887 °2
S-0.0194 Å °0.0108 Å °0.054 Å °-0.0383 Å °-0.0107 Å °0.042 Å °-0.0986 Å °-0.0405 Å °0.026 Å °
Refinement TLS groupSelection details: all

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