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- PDB-6erb: Enterococcus faecalis FIC protein (H111A) in complex with sulfate. -

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Basic information

Entry
Database: PDB / ID: 6erb
TitleEnterococcus faecalis FIC protein (H111A) in complex with sulfate.
ComponentsFic family protein
KeywordsTOXIN
Function / homologyFido-like domain / Fic-like fold / Fido-like domain superfamily / Fic/DOC family / Fido domain / Fido domain profile. / Orthogonal Bundle / Mainly Alpha / Fic family protein
Function and homology information
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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 1.2Mar 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 1.3Sep 25, 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.details / _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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)98,6608
Polymers98,2764
Non-polymers3844
Water5,296294
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5660 Å2
ΔGint-86 kcal/mol
Surface area36560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.931, 131.161, 136.711
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-413-

HOH

21A-468-

HOH

31A-484-

HOH

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Components

#1: Protein
Fic family protein


Mass: 24569.047 Da / Num. of mol.: 4
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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 294 / 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: 2.77 Å3/Da / Density % sol: 55.65 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 50mM Tris pH 8.0, 150mM NaCl, 2mM ATPgS, 2mM MgCl2, 0.2M Lithium Sulfate, 0.1M Tris pH 8.5, 20% (w/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.980112 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.980112 Å / Relative weight: 1
ReflectionResolution: 2.2→47.32 Å / Num. obs: 55829 / % possible obs: 100 % / Redundancy: 13.7 % / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.032 / Net I/σ(I): 18.5
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 14.2 % / Rmerge(I) obs: 1.321 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4558 / Rpim(I) all: 0.526 / % possible all: 100

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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: 2G03

2g03


Resolution: 2.2→43.046 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2488 2733 4.9 %
Rwork0.2132 --
obs0.215 55793 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→43.046 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6596 0 20 294 6910
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086737
X-RAY DIFFRACTIONf_angle_d1.0129070
X-RAY DIFFRACTIONf_dihedral_angle_d17.0434108
X-RAY DIFFRACTIONf_chiral_restr0.058972
X-RAY DIFFRACTIONf_plane_restr0.0071168
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.23790.38621520.33122630X-RAY DIFFRACTION100
2.2379-2.27860.34261290.33162601X-RAY DIFFRACTION100
2.2786-2.32240.39691600.30712574X-RAY DIFFRACTION100
2.3224-2.36990.42631410.29212645X-RAY DIFFRACTION100
2.3699-2.42140.29541340.27872623X-RAY DIFFRACTION100
2.4214-2.47770.32121450.2722611X-RAY DIFFRACTION100
2.4777-2.53970.32231360.27172630X-RAY DIFFRACTION100
2.5397-2.60830.31221300.25582637X-RAY DIFFRACTION100
2.6083-2.68510.29841070.26192671X-RAY DIFFRACTION100
2.6851-2.77170.28831230.26172636X-RAY DIFFRACTION100
2.7717-2.87070.3611230.27262645X-RAY DIFFRACTION100
2.8707-2.98570.28911250.25992676X-RAY DIFFRACTION100
2.9857-3.12150.28941450.26232642X-RAY DIFFRACTION100
3.1215-3.2860.28111730.2442601X-RAY DIFFRACTION100
3.286-3.49180.24111430.22732650X-RAY DIFFRACTION100
3.4918-3.76130.2557910.20262712X-RAY DIFFRACTION100
3.7613-4.13950.23091190.18442687X-RAY DIFFRACTION100
4.1395-4.73790.19021520.16052675X-RAY DIFFRACTION100
4.7379-5.96670.18221570.17162699X-RAY DIFFRACTION100
5.9667-43.05440.19621480.1612815X-RAY DIFFRACTION100

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