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- PDB-6ep0: Enterococcus faecalis FIC protein in complex with AMP and calcium ion. -

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Basic information

Entry
Database: PDB / ID: 6ep0
TitleEnterococcus faecalis FIC protein in complex with AMP 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 MONOPHOSPHATE / Fic family protein
Similarity search - Component
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 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 / database_PDB_rev ...citation / database_PDB_rev / database_PDB_rev_record / 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 / software / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _software.name / _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.ptnr1_symmetry / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,27812
Polymers49,2722
Non-polymers1,00610
Water2,396133
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4620 Å2
ΔGint-86 kcal/mol
Surface area18130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.975, 64.975, 246.239
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Fic family protein


Mass: 24636.117 Da / Num. of mol.: 2
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-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / 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: 2.64 Å3/Da / Density % sol: 53.36 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 50mM Tris pH 8.0, 100mM NaCl, 5mM AMP, 0.2M Calcium Chloride, 0.1M HEPES sodium salt pH 7.5, 28% (v/v) PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976247 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976247 Å / Relative weight: 1
ReflectionResolution: 2.35→82.08 Å / Num. obs: 23042 / % possible obs: 100 % / Redundancy: 16.7 % / Biso Wilson estimate: 62.34 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.139 / Rpim(I) all: 0.048 / Net I/σ(I): 13.1
Reflection shellResolution: 2.35→2.48 Å / Redundancy: 17.8 % / Rmerge(I) obs: 1.146 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 3273 / CC1/2: 0.925 / Rpim(I) all: 0.39 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
autoPROCdata scaling
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5NUW

5nuw
PDB Unreleased entry


Resolution: 2.35→62.82 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.924 / SU R Cruickshank DPI: 0.323 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.347 / SU Rfree Blow DPI: 0.246 / SU Rfree Cruickshank DPI: 0.243
RfactorNum. reflection% reflectionSelection details
Rfree0.264 1132 4.93 %RANDOM
Rwork0.218 ---
obs0.22 22951 99.7 %-
Displacement parametersBiso mean: 61.1 Å2
Baniso -1Baniso -2Baniso -3
1--5.7147 Å20 Å20 Å2
2---5.7147 Å20 Å2
3---11.4294 Å2
Refinement stepCycle: 1 / Resolution: 2.35→62.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3334 0 54 130 3518
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013454HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.084659HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1281SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes106HARMONIC2
X-RAY DIFFRACTIONt_gen_planes508HARMONIC5
X-RAY DIFFRACTIONt_it3454HARMONIC20
X-RAY DIFFRACTIONt_nbd5SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.94
X-RAY DIFFRACTIONt_other_torsion19.47
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion437SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4158SEMIHARMONIC4
LS refinement shellResolution: 2.35→2.45 Å / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.2934 123 4.64 %
Rwork0.2468 2530 -
all0.249 2653 -
obs--97.13 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.5263-0.22311.2650.6856-0.16363.39090.0404-0.3387-0.1406-0.02690.0738-0.1180.0041-0.2617-0.1142-0.1414-0.0286-0.01390.00670.0666-0.0448-10.236928.917511.0845
22.1243-0.1567-0.31250.9462-0.04921.5562-0.0938-0.5442-0.123-0.00660.09940.13130.10360.3542-0.0056-0.19980.0178-0.01170.25090.0091-0.1526-36.012736.640723.6857
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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