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- PDB-4glk: Structure and activity of AbiQ, a lactococcal anti-phage endoribo... -

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Basic information

Entry
Database: PDB / ID: 4glk
TitleStructure and activity of AbiQ, a lactococcal anti-phage endoribonuclease belonging to the type-III toxin-antitoxin system
ComponentsAbiQ
KeywordsHYDROLASE / Alpha Beta / endonuclease / RNA antiQ
Function / homology
Function and homology information


RNA endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / RNA binding / cytoplasm
Similarity search - Function
ToxN/AbiQ toxin / Toxin ToxN, type III toxin-antitoxin system / Thiol Ester Dehydrase; Chain A - #130 / Thiol Ester Dehydrase; Chain A / Roll / Alpha Beta
Similarity search - Domain/homology
Endoribonuclease AbiQ
Similarity search - Component
Biological speciesLactococcus lactis (lactic acid bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.16 Å
AuthorsSamson, J. / Spinelli, S. / Cambillau, C. / Moineau, S.
CitationJournal: Mol.Microbiol. / Year: 2013
Title: Structure and activity of AbiQ, a lactococcal endoribonuclease belonging to the type III toxin-antitoxin system.
Authors: Samson, J.E. / Spinelli, S. / Cambillau, C. / Moineau, S.
History
DepositionAug 14, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2013Group: Database references
Revision 1.2Sep 13, 2023Group: 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AbiQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5854
Polymers20,3091
Non-polymers2763
Water1,24369
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.140, 54.510, 64.240
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein AbiQ


Mass: 20308.732 Da / Num. of mol.: 1 / Fragment: UNP residues 13-183 / Mutation: S51L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactococcus lactis (lactic acid bacteria)
Gene: abiQ / Plasmid: pDEST17 / Production host: Escherichia coli (E. coli) / Strain (production host): K12
References: UniProt: Q9ZJ19, Hydrolases; Acting on ester bonds
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 2.16 Å3/Da / Density % sol: 43.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: buffer: 1 M potassium/sodium tartrate, 0.1 M MES, pH 6.0, drop: 200 nL 4.6 mg/mL protein + 100 nL buffer, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9791 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 14, 2011
RadiationMonochromator: channel cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.16→45 Å / Num. all: 9880 / Num. obs: 9880 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.7 % / Biso Wilson estimate: 35.49 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 17.1
Reflection shellResolution: 2.16→2.22 Å / Redundancy: 13.1 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 3.7 / Num. unique all: 753 / % possible all: 99.6

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Processing

Software
NameVersionClassification
DNAdata collection
MOLREPphasing
BUSTER2.9.2refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XDD

2xdd


Resolution: 2.16→27.67 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.9239 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2232 694 7.02 %RANDOM
Rwork0.1937 ---
all0.1958 9880 --
obs0.1958 9880 --
Displacement parametersBiso mean: 38.47 Å2
Baniso -1Baniso -2Baniso -3
1-6.209 Å20 Å20 Å2
2--5.4018 Å20 Å2
3----11.6108 Å2
Refine analyzeLuzzati coordinate error obs: 0.272 Å
Refinement stepCycle: LAST / Resolution: 2.16→27.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1353 0 18 69 1440
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0091397HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.181876HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d0493SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes028HARMONIC2
X-RAY DIFFRACTIONt_gen_planes0195HARMONIC5
X-RAY DIFFRACTIONt_it01397HARMONIC20
X-RAY DIFFRACTIONt_omega_torsion3.77
X-RAY DIFFRACTIONt_other_torsion23.96
X-RAY DIFFRACTIONt_chiral_improper_torsion0177SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact01651SEMIHARMONIC4
LS refinement shellResolution: 2.16→2.42 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.3178 173 6.33 %
Rwork0.2274 2561 -
all0.2327 2734 -
obs-2734 -
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)
10.5346-0.14210.12810.0035-0.00910.14010.00340.0205-0.01050.0346-0.0029-0.01110.0164-0.0004-0.0005-0.0153-0.01780.00630.006-0.0282-0.0027-4.2379.7849-8.4216
20.16130.0871-0.05680.3875-0.15450.383-0.00290.01610.01390.0236-0.01570-0.0024-0.01430.01860.0082-0.00380.0308-0.0168-0.01910.0187-11.603512.135-3.6199
30.1406-0.0553-0.38070-0.48880.3075-0.0004-0.0013-0.0027-0.00190.005-0.0108-0.00770.0019-0.0045-0.00710.0615-0.01270.02090.01260.01154.602915.8531-10.3077
40.19540.3321-0.06180.36490.81370.2286-0.0020.02010.0047-0.00420.02140.00750.0064-0.0228-0.0194-0.00810.0079-0.0156-0.0048-0.00960.0087-7.976519.0957-13.6104
50.0636-0.04390.05870-0.17710.00030-0.00230.00250.0052-0.00390.00490.0003-0.00810.0039-0.02430.0129-0.03940.01630.02230.001-14.624231.173-12.7675
60.31860.40460.04070.041-0.46690.12170.00610.00660.002-0.0054-0.00470.0243-0.00760.003-0.0014-0.0198-0.0051-0.02290.02560.038-0.0036-8.35327.3597-21.7348
70.28750.0482-0.370.3091-0.14930.27790.0021-0.00230.0168-0.0208-0.00720.0173-0.0135-0.00420.0051-0.02330.00690.00450.01410.02290.0057-9.141824.1527-15.855
80.0817-0.55860.029800.32230.0341-0.00390.00360.0110.0148-0.0004-0.01370.01330.00530.00430.00180.0183-0.0318-0.0219-0.03050.0214-1.49327.349-10.2771
90.31860.10420.33290.3591-0.174700.00090.0059-0.00020.00730.00050.0118-0.0041-0.019-0.0014-0.0066-0.006-0.0793-0.0135-0.01130.0399-13.710410.3151-25.7781
100.07370.1287-0.1610.0018-0.40350.23940.0048-0.0021-0.0018-0.03680.00230.00190.0030.0105-0.00710.0122-0.0126-0.013-0.0280.01610.007-2.219121.6364-23.4358
110.0656-0.10760.24720.2088-0.08070.0209-0.0012-0.0013-0.01690.00670.0092-0.00940.00070.0146-0.0079-0.0263-0.0124-0.0141-0.01450.01810.05274.588727.1871-7.8214
120.0465-0.10370.58070.02140.13990.01810.0023-0.00090.00690.020.005-0.0118-0.00040.0032-0.0073-0.00770.0234-0.04040.0221-0.0192-0.0246-2.054329.2585-1.0962
130.0070.22510.6630.1256-0.26370.113-0.0017-0.011-0.0170.01140.001-0.00340.0040.00730.00070.03050.0221-0.10950.0120.01920.00143.562210.59322.3426
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|1 - A|17}A1 - 17
2X-RAY DIFFRACTION2{A|18 - A|33}A18 - 33
3X-RAY DIFFRACTION3{A|34 - A|44}A34 - 44
4X-RAY DIFFRACTION4{A|45 - A|57}A45 - 57
5X-RAY DIFFRACTION5{A|58 - A|68}A58 - 68
6X-RAY DIFFRACTION6{A|69 - A|80}A69 - 80
7X-RAY DIFFRACTION7{A|81 - A|92}A81 - 92
8X-RAY DIFFRACTION8{A|93 - A|104}A93 - 104
9X-RAY DIFFRACTION9{A|105 - A|116}A105 - 116
10X-RAY DIFFRACTION10{A|117 - A|129}A117 - 129
11X-RAY DIFFRACTION11{A|130 - A|142}A130 - 142
12X-RAY DIFFRACTION12{A|143 - A|155}A143 - 155
13X-RAY DIFFRACTION13{A|156 - A|168}A156 - 168

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