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- PDB-5nv5: Enterococcus faecalis FIC protein -

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Basic information

Entry
Database: PDB / ID: 5nv5
TitleEnterococcus faecalis FIC protein
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: 2.4 Å
AuthorsVeyron, S. / Cherfils, J.
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
DepositionMay 3, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 30, 2018Provider: 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 1.3Oct 16, 2019Group: Data collection / Category: reflns_shell
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
C: Fic family protein
D: Fic family protein


Theoretical massNumber of molelcules
Total (without water)98,5444
Polymers98,5444
Non-polymers00
Water12,124673
1
A: Fic family protein


Theoretical massNumber of molelcules
Total (without water)24,6361
Polymers24,6361
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Fic family protein


Theoretical massNumber of molelcules
Total (without water)24,6361
Polymers24,6361
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Fic family protein


Theoretical massNumber of molelcules
Total (without water)24,6361
Polymers24,6361
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Fic family protein


Theoretical massNumber of molelcules
Total (without water)24,6361
Polymers24,6361
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)121.541, 131.001, 136.935
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-411-

HOH

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Components

#1: Protein
Fic family protein


Mass: 24636.117 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 673 / 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: 55.53 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 10mM Hepes pH 7,4, 200mM NaCl, 50mM Bicine pH 8.4, 30% (w/v) PEG 2000 MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Nov 7, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.4→47.33 Å / Num. obs: 42957 / % possible obs: 99.7 % / Redundancy: 5.6 % / Biso Wilson estimate: 51.22 Å2 / Net I/σ(I): 13.5

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHENIXphasing
BUSTER2.10.2refinement
PHENIXrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5NUW

5nuw
PDB Unreleased entry


Resolution: 2.4→47.33 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.913 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.287 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.327 / SU Rfree Blow DPI: 0.229 / SU Rfree Cruickshank DPI: 0.224
RfactorNum. reflection% reflectionSelection details
Rfree0.226 2116 4.93 %RANDOM
Rwork0.164 ---
obs0.167 42957 99.8 %-
Displacement parametersBiso mean: 50.53 Å2
Baniso -1Baniso -2Baniso -3
1--11.699 Å20 Å20 Å2
2--1.599 Å20 Å2
3---10.1001 Å2
Refine analyzeLuzzati coordinate error obs: 0 Å
Refinement stepCycle: 1 / Resolution: 2.4→47.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6637 0 0 675 7312
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.016759HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.089098HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2500SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes209HARMONIC2
X-RAY DIFFRACTIONt_gen_planes948HARMONIC5
X-RAY DIFFRACTIONt_it6759HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.13
X-RAY DIFFRACTIONt_other_torsion18.56
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion854SEMIHARMONIC5
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_contact8238SEMIHARMONIC4
LS refinement shellResolution: 2.4→2.46 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 162 5.22 %
Rwork0.217 2943 -
all0.221 3105 -
obs--98.53 %
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)
11.56-0.0061-0.65841.4707-0.32762.2153-0.0888-0.1566-0.17260.08580.092-0.0201-0.0988-0.0732-0.0032-0.12240.02040.0537-0.02780.021-0.053148.384238.1203149.222
20.65680.80580.21214.42990.21381.2011-0.029-0.07570.0660.3340.0070.0438-0.04830.01770.0220.1262-0.00330.0086-0.14680.0057-0.119437.390373.8796163.202
31.54920.4951-0.70532.177-0.57132.57240.00930.0970.09860.14970.01890.1102-0.1926-0.2723-0.0282-0.14-0.0004-0.0133-0.01030.0163-0.086615.342239.3448150.428
42.34490.42490.31812.5294-0.9033.7180.2155-0.24850.23220.3014-0.27160.0259-0.44040.24080.05610.1207-0.07970.0565-0.1244-0.0132-0.181830.248648.5776186.687
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }

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