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- PDB-5ecd: Structure of the Shigella flexneri VapC mutant D98N crystal form 1 -

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Basic information

Entry
Database: PDB / ID: 5ecd
TitleStructure of the Shigella flexneri VapC mutant D98N crystal form 1
ComponentstRNA(fMet)-specific endonuclease VapC
KeywordsHYDROLASE / Toxin / PIN-domain / Hepes
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: 1.75 Å
AuthorsXu, K.
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 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

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Assembly

Deposited unit
A: tRNA(fMet)-specific endonuclease VapC
B: tRNA(fMet)-specific endonuclease VapC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8054
Polymers31,3282
Non-polymers4772
Water4,864270
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2930 Å2
ΔGint-12 kcal/mol
Surface area11910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.450, 121.450, 51.740
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-441-

HOH

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Components

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


Mass: 15663.973 Da / Num. of mol.: 2 / 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: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 270 / 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: 2.34 Å3/Da / Density % sol: 47.53 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 20% PEG 3350, 0.2M sodium malonate, NaOH-Hepes, pH7.0

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Data collection

DiffractionMean temperature: 80 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: 1.75→25.41 Å / Num. obs: 2917 / % possible obs: 99.9 % / Redundancy: 3.84 % / Net I/σ(I): 15.69

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Processing

Software
NameVersionClassification
PHENIXdev_1839refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→25.41 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1972 2005 6.98 %
Rwork0.1609 --
obs0.1635 28707 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.75→25.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2040 0 30 270 2340
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072130
X-RAY DIFFRACTIONf_angle_d0.9372878
X-RAY DIFFRACTIONf_dihedral_angle_d14.259810
X-RAY DIFFRACTIONf_chiral_restr0.042323
X-RAY DIFFRACTIONf_plane_restr0.004373
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.79380.3281460.31271949X-RAY DIFFRACTION100
1.7938-1.84230.30631450.28171885X-RAY DIFFRACTION100
1.8423-1.89650.31631420.25531903X-RAY DIFFRACTION100
1.8965-1.95770.28791390.22661913X-RAY DIFFRACTION100
1.9577-2.02760.27961440.20721902X-RAY DIFFRACTION100
2.0276-2.10880.20551410.18231910X-RAY DIFFRACTION100
2.1088-2.20470.21461420.17591897X-RAY DIFFRACTION100
2.2047-2.32090.23811420.1711915X-RAY DIFFRACTION100
2.3209-2.46630.21951440.16871915X-RAY DIFFRACTION100
2.4663-2.65660.20891430.15881895X-RAY DIFFRACTION100
2.6566-2.92380.19441450.16431897X-RAY DIFFRACTION100
2.9238-3.34640.18261400.1541904X-RAY DIFFRACTION100
3.3464-4.21430.16131450.12291920X-RAY DIFFRACTION100
4.2143-30.36710.13351470.12181897X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -24.1057 Å / Origin y: -7.8213 Å / Origin z: 20.3833 Å
111213212223313233
T0.1834 Å20.0323 Å20.0206 Å2-0.1601 Å20.0013 Å2--0.1812 Å2
L2.8946 °20.3338 °2-1.4031 °2-0.6029 °2-0.1312 °2--1.8425 °2
S-0.2936 Å °-0.1492 Å °-0.3741 Å °0.0418 Å °0.0443 Å °-0.0068 Å °0.2344 Å °0.1444 Å °0.1641 Å °
Refinement TLS groupSelection details: all

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