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- PDB-6er8: Enterococcus faecalis FIC protein in complex with phosphate. -

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Basic information

Entry
Database: PDB / ID: 6er8
TitleEnterococcus faecalis FIC protein in complex with phosphate.
ComponentsFic family protein
KeywordsTOXIN / FIC / AMPylation
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
ACETATE ION / PHOSPHATE ION / Fic family protein
Similarity search - Component
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.292 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 17, 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 1.2Aug 28, 2019Group: Data collection / Database references / Category: citation / citation_author
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 1.3Sep 4, 2019Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: entity / entity_src_gen ...entity / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity_src_gen.gene_src_common_name ..._entity.pdbx_description / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_gene / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.pdbx_seq_db_accession_code
Revision 1.4Jan 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5215
Polymers49,2722
Non-polymers2493
Water5,314295
1
A: Fic family protein
B: Fic family protein
hetero molecules

A: Fic family protein
B: Fic family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,04210
Polymers98,5444
Non-polymers4986
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_465y-1,x+1,-z1
Buried area8600 Å2
ΔGint-36 kcal/mol
Surface area33850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.130, 65.130, 248.060
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-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 295 / 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: 2.67 Å3/Da / Density % sol: 53.92 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 50mM Tris pH 8.0, 200mM NaCl, 1mM MgCl2, 0.2M Ammonium sulfate, 0.1M Tris-sodium citrate pH 5.6, 15% (w:v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.29→44.91 Å / Num. obs: 23660 / % possible obs: 94.8 % / Redundancy: 4 % / Rmerge(I) obs: 0.312 / Net I/σ(I): 5.2
Reflection shellResolution: 2.29→2.38 Å / Redundancy: 2.8 % / Rmerge(I) obs: 1.808 / Num. unique obs: 2338 / % possible all: 91.7

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2G03

2g03


Resolution: 2.292→44.91 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 31.46
RfactorNum. reflection% reflection
Rfree0.2987 1179 5 %
Rwork0.2291 --
obs0.2326 23562 94.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.292→44.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3344 0 14 295 3653
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083417
X-RAY DIFFRACTIONf_angle_d0.8934599
X-RAY DIFFRACTIONf_dihedral_angle_d14.7692074
X-RAY DIFFRACTIONf_chiral_restr0.05491
X-RAY DIFFRACTIONf_plane_restr0.005592
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2924-2.39670.39141410.32312682X-RAY DIFFRACTION92
2.3967-2.52310.39681470.29562789X-RAY DIFFRACTION96
2.5231-2.68110.33271470.2842788X-RAY DIFFRACTION96
2.6811-2.88810.33461460.26862780X-RAY DIFFRACTION95
2.8881-3.17870.34391470.24312782X-RAY DIFFRACTION95
3.1787-3.63840.27111480.18882822X-RAY DIFFRACTION94
3.6384-4.58330.24111490.16642828X-RAY DIFFRACTION94
4.5833-44.92070.27671540.24382912X-RAY DIFFRACTION91

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