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- PDB-5urp: Plx2a, an ADP-ribosyltransferase toxin from Paenibacillus larvae -

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Basic information

Entry
Database: PDB / ID: 5urp
TitlePlx2a, an ADP-ribosyltransferase toxin from Paenibacillus larvae
ComponentsToxin 2A
KeywordsTOXIN / transferase / virulence factor
Function / homology
Function and homology information


: / extracellular region
Similarity search - Function
Binary exotoxin A, clostridial type / Toxin ADP-ribosyltransferase; Chain A, domain 1 / Toxin ADP-ribosyltransferase; Chain A, domain 1 / ADP ribosyltransferase / ADP-ribosyltransferase exoenzyme / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Biological speciesPaenibacillus larvae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsRavulapalli, R. / Heney, K. / Ebeling, J. / Genersch, E. / Merrill, A.R.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)MOP-106661 Canada
CitationJournal: Environ.Microbiol. / Year: 2017
Title: Structural and functional characterization of Plx2a, an ADP-ribosyltransferase toxin from Paenibacillus larvae
Authors: Ravulapalli, R. / Heney, K. / Ebeling, J. / Genersch, E. / Merrill, A.R.
History
DepositionFeb 12, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 4, 2023Group: 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: Toxin 2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5592
Polymers25,4671
Non-polymers921
Water2,918162
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.920, 53.970, 98.180
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 Toxin 2A


Mass: 25467.363 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paenibacillus larvae (bacteria) / Gene: plx2A / Plasmid: pET28b-TEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 lamda DE3 / References: UniProt: M9V3B7
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / 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: 2.44 Å3/Da / Density % sol: 49.6 %
Crystal growTemperature: 294 K / Method: vapor diffusion / Details: 4M Sodium Formate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.979 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Aug 15, 2015
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.65→49.09 Å / Num. obs: 30729 / % possible obs: 100 % / Redundancy: 6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.056 / Net I/σ(I): 15.71
Reflection shellResolution: 1.65→1.709 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.929 / Mean I/σ(I) obs: 1.71 / Num. unique obs: 3022 / CC1/2: 0.757 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4TR5

4tr5


Resolution: 1.65→49.09 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.18
RfactorNum. reflection% reflection
Rfree0.1996 1537 5 %
Rwork0.1716 --
obs0.1731 30712 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.65→49.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1613 0 6 162 1781
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011657
X-RAY DIFFRACTIONf_angle_d1.0822219
X-RAY DIFFRACTIONf_dihedral_angle_d15.4761028
X-RAY DIFFRACTIONf_chiral_restr0.064246
X-RAY DIFFRACTIONf_plane_restr0.007276
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.70330.34431380.29062609X-RAY DIFFRACTION100
1.7033-1.76410.2661370.25922602X-RAY DIFFRACTION100
1.7641-1.83480.28221380.23142618X-RAY DIFFRACTION100
1.8348-1.91830.21971370.19292610X-RAY DIFFRACTION100
1.9183-2.01940.2031380.17912621X-RAY DIFFRACTION100
2.0194-2.1460.18751390.17432639X-RAY DIFFRACTION100
2.146-2.31160.21441390.16412631X-RAY DIFFRACTION100
2.3116-2.54430.19121390.15992650X-RAY DIFFRACTION100
2.5443-2.91240.19851410.17782666X-RAY DIFFRACTION100
2.9124-3.66910.20621420.16652702X-RAY DIFFRACTION100
3.6691-49.11170.17381490.15432827X-RAY DIFFRACTION100
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)
12.44290.851-1.45336.2308-5.19996.2743-0.0234-0.1163-0.5037-0.0788-0.5974-1.18580.15020.76240.53630.24320.06070.05150.36540.03690.38369.4638-16.70612.0373
26.46750.0241.15314.2169-0.40614.25790.1227-0.02110.30440.0016-0.0350.3524-0.5354-0.5875-0.02540.25050.0609-0.00340.2212-0.01680.1906-5.11380.825412.7321
32.92910.5451-2.85333.55412.9737.74420.21240.08771.1101-0.5320.0628-0.1615-1.0823-0.1286-0.22480.41650.0656-0.00420.2610.03620.3532-2.99842.34526.1781
43.94191.2360.03893.368-1.04484.4327-0.0102-0.38960.26170.02010.19580.54740.0503-0.7477-0.12570.23660.0309-0.01770.32070.02560.3118-15.2547-20.716515.538
51.94581.07280.22562.3216-0.70721.9005-0.04190.0563-0.057-0.110.10770.04390.1246-0.1243-0.05060.21070.0165-0.0060.232-0.00450.204-6.1578-17.578213.1464
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 25 )
2X-RAY DIFFRACTION2chain 'A' and (resid 26 through 56 )
3X-RAY DIFFRACTION3chain 'A' and (resid 57 through 72 )
4X-RAY DIFFRACTION4chain 'A' and (resid 73 through 116 )
5X-RAY DIFFRACTION5chain 'A' and (resid 117 through 201 )

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