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- PDB-5ecy: Structure of the Shigella flexneri VapC mutant D98N crystal form 2 -

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Basic information

Entry
Database: PDB / ID: 5ecy
TitleStructure of the Shigella flexneri VapC mutant D98N crystal form 2
ComponentstRNA(fMet)-specific endonuclease VapC
KeywordsHYDROLASE / Toxin / PIN-domain
Function / homology
Function and homology information


RNA nuclease activity / endonuclease activity / Hydrolases; Acting on ester bonds / magnesium ion binding
Similarity search - Function
: / PIN domain / VapC family / 5'-nuclease / PIN domain / PIN-like domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
tRNA(fMet)-specific endonuclease VapC
Similarity search - Component
Biological speciesShigella flexneri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsXu, K. / Dedic, E. / Brodersen, D.E.
Funding support China, 1items
OrganizationGrant numberCountry
Chinese Scholarship Council China
CitationJournal: to be published
Title: Structural analysis on the active site architecture of an activated VapC toxin from Shigella flexneri
Authors: Xu, K. / Dedic, E. / Brodersen, D.E.
History
DepositionOct 20, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 19, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 2.0May 8, 2024Group: Atomic model / Data collection / Database references
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2
Item: _atom_site.occupancy / _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: tRNA(fMet)-specific endonuclease VapC
B: tRNA(fMet)-specific endonuclease VapC
C: tRNA(fMet)-specific endonuclease VapC
D: tRNA(fMet)-specific endonuclease VapC
E: tRNA(fMet)-specific endonuclease VapC
F: tRNA(fMet)-specific endonuclease VapC
G: tRNA(fMet)-specific endonuclease VapC
H: tRNA(fMet)-specific endonuclease VapC


Theoretical massNumber of molelcules
Total (without water)125,3128
Polymers125,3128
Non-polymers00
Water22,6811259
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14890 Å2
ΔGint-79 kcal/mol
Surface area42430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.440, 139.440, 130.660
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-316-

HOH

21A-333-

HOH

31F-257-

HOH

41F-329-

HOH

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Components

#1: Protein
tRNA(fMet)-specific endonuclease VapC / RNase VapC / Toxin VapC


Mass: 15663.973 Da / Num. of mol.: 8 / Mutation: D98N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella flexneri (bacteria) / Gene: vapC, mvpA, stborf2, CP0245 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: O06662, Hydrolases; Acting on ester bonds
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1259 / 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: 2.53 Å3/Da / Density % sol: 51.46 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 2.8 M sodium acetate trihydrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 0.9795 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2→47.67 Å / Num. obs: 8429 / % possible obs: 100 % / Redundancy: 9.76 % / Net I/σ(I): 8.71

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Processing

Software
NameVersionClassification
PHENIXdev_1839refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementResolution: 2→47.67 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.65 / Phase error: 20.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2138 1998 2.3 %
Rwork0.1797 --
obs0.1805 86931 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→47.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8274 0 0 1259 9533
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0098481
X-RAY DIFFRACTIONf_angle_d1.07211434
X-RAY DIFFRACTIONf_dihedral_angle_d12.1813220
X-RAY DIFFRACTIONf_chiral_restr0.0531283
X-RAY DIFFRACTIONf_plane_restr0.0061507
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.28641480.27855848X-RAY DIFFRACTION98
2.05-2.10540.32431210.24215992X-RAY DIFFRACTION100
2.1054-2.16740.26441480.22716014X-RAY DIFFRACTION100
2.1674-2.23730.24791440.20635982X-RAY DIFFRACTION100
2.2373-2.31730.23181340.20156026X-RAY DIFFRACTION100
2.3173-2.41010.25511400.1966024X-RAY DIFFRACTION100
2.4101-2.51970.28491380.19926038X-RAY DIFFRACTION100
2.5197-2.65260.22981500.18776023X-RAY DIFFRACTION100
2.6526-2.81880.25071440.18396070X-RAY DIFFRACTION100
2.8188-3.03640.19311390.17076092X-RAY DIFFRACTION100
3.0364-3.34180.18041470.16016075X-RAY DIFFRACTION100
3.3418-3.82520.15791440.14116133X-RAY DIFFRACTION100
3.8252-4.81870.1521430.13516202X-RAY DIFFRACTION100
4.8187-47.68530.2081580.17976414X-RAY DIFFRACTION99

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