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- PDB-5ecw: Structure of the Shigella flexneri VapC mutant D7A -

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Basic information

Entry
Database: PDB / ID: 5ecw
TitleStructure of the Shigella flexneri VapC mutant D7A
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 / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsXu, K. / Dedic, E. / Brodersen, D.E.
Funding support China, 1items
OrganizationGrant numberCountry
Chinese Scholarship Council China
CitationJournal: Proteins / Year: 2016
Title: Structural analysis of the active site architecture of the VapC toxin from Shigella flexneri.
Authors: Xu, K. / Dedic, E. / Brodersen, D.E.
History
DepositionOct 20, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 17, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 15, 2016Group: Database references
Revision 1.2Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: tRNA(fMet)-specific endonuclease VapC
B: tRNA(fMet)-specific endonuclease VapC


Theoretical massNumber of molelcules
Total (without water)31,2422
Polymers31,2422
Non-polymers00
Water1,76598
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2210 Å2
ΔGint-21 kcal/mol
Surface area11650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.100, 120.100, 52.530
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

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


Mass: 15620.947 Da / Num. of mol.: 2 / Mutation: D7A
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.: 98 / 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: 2.33 Å3/Da / Density % sol: 47.15 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.2 M sodium malonate, 20% PEG 3350

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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: Dec 12, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.94→23.44 Å / Num. obs: 1751 / % possible obs: 92.4 % / Redundancy: 6.25 % / Net I/σ(I): 30.77

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Processing

Software
NameVersionClassification
PHENIXdev_1839refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.94→23.44 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 26.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2259 1925 9.96 %
Rwork0.1888 --
obs0.1925 19319 92.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.94→23.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1919 0 0 98 2017
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081955
X-RAY DIFFRACTIONf_angle_d1.0022640
X-RAY DIFFRACTIONf_dihedral_angle_d13.306711
X-RAY DIFFRACTIONf_chiral_restr0.046305
X-RAY DIFFRACTIONf_plane_restr0.005344
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.94-1.98850.61551200.59541071X-RAY DIFFRACTION79
1.9885-2.04230.26761460.23561337X-RAY DIFFRACTION100
2.0423-2.10230.28031550.21961369X-RAY DIFFRACTION100
2.1023-2.17020.27531410.20211310X-RAY DIFFRACTION100
2.1702-2.24770.2587910.2168806X-RAY DIFFRACTION97
2.2477-2.33760.2705910.2282821X-RAY DIFFRACTION96
2.3376-2.44390.24411470.20291342X-RAY DIFFRACTION100
2.4439-2.57270.24561490.20551352X-RAY DIFFRACTION100
2.5727-2.73370.26861500.19881343X-RAY DIFFRACTION100
2.7337-2.94440.26441490.20661330X-RAY DIFFRACTION100
2.9444-3.24020.25011490.20331347X-RAY DIFFRACTION100
3.2402-3.70780.21991510.17891353X-RAY DIFFRACTION100
3.7078-4.66660.16521470.14531337X-RAY DIFFRACTION100
4.6666-25.28740.17471390.16221276X-RAY DIFFRACTION94
Refinement TLS params.Method: refined / Origin x: -23.8041 Å / Origin y: -7.3765 Å / Origin z: 13.5334 Å
111213212223313233
T0.3183 Å20.0841 Å2-0.0215 Å2-0.2823 Å2-0.0277 Å2--0.2039 Å2
L7.2223 °20.3473 °2-2.3881 °2-1.6086 °2-0.0421 °2--2.8054 °2
S-0.6098 Å °-0.3808 Å °-0.3815 Å °0.1388 Å °0.2567 Å °0.0487 Å °0.3384 Å °0.2283 Å °0.228 Å °
Refinement TLS groupSelection details: all

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