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- PDB-5dzq: C3larvin toxin, an ADP-ribosyltransferase from Paenibacillus larv... -

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Basic information

Entry
Database: PDB / ID: 5dzq
TitleC3larvin toxin, an ADP-ribosyltransferase from Paenibacillus larvae, Orthorhombic Form
ComponentsToxin-like protein
KeywordsTRANSFERASE
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 / Toxin-related mono-ADP-ribosyltransferase (TR mART) core domain profile. / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Biological speciesPaenibacillus larvae subsp. larvae BRL-230010 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.892 Å
AuthorsDutta, D. / Ravulapalli, R. / Merrill, A.R.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: J. Biomol. Struct. Dyn. / Year: 2016
Title: Structural variability of C3larvin toxin. Intrinsic dynamics of the alpha / beta fold of the C3-like group of mono-ADP-ribosyltransferase toxins.
Authors: Lugo, M.R. / Ravulapalli, R. / Dutta, D. / Merrill, A.R.
History
DepositionSep 26, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2017Group: Database references
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Feb 14, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 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-like protein
O: Toxin-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6316
Polymers49,3982
Non-polymers2334
Water1,892105
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2430 Å2
ΔGint-10 kcal/mol
Surface area19750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.073, 76.002, 89.367
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-like protein / C3larvin


Mass: 24699.217 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paenibacillus larvae subsp. larvae BRL-230010 (bacteria)
Gene: ERIC1_2c04930 / Production host: Escherichia coli (E. coli) / References: UniProt: W2E3J5, NAD+ ADP-ribosyltransferase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 105 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 41.41 %
Crystal growTemperature: 297.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2 M magnesium chloride hexahydrate, 0.1 M Tris-HCl, 30% w/v PEG4000
PH range: 8.5

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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: May 1, 2014
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: 1.89→47.61 Å / Num. obs: 33554 / % possible obs: 98.9 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.045 / Net I/σ(I): 25.22
Reflection shellResolution: 1.89→1.96 Å / % possible all: 89.64

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
REFMAC5.8.0073refinement
XSCALEdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4TR5

4tr5


Resolution: 1.892→47.607 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 23.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2302 1678 5 %
Rwork0.1929 --
obs0.1948 33552 98.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.892→47.607 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2946 0 14 105 3065
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073013
X-RAY DIFFRACTIONf_angle_d1.0224034
X-RAY DIFFRACTIONf_dihedral_angle_d14.6821186
X-RAY DIFFRACTIONf_chiral_restr0.042437
X-RAY DIFFRACTIONf_plane_restr0.004508
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8916-1.94730.29321220.25872325X-RAY DIFFRACTION88
1.9473-2.01020.27591370.21072595X-RAY DIFFRACTION99
2.0102-2.0820.29341410.20552675X-RAY DIFFRACTION100
2.082-2.16540.2471390.19042657X-RAY DIFFRACTION100
2.1654-2.26390.24951390.19192641X-RAY DIFFRACTION100
2.2639-2.38330.24961410.2022660X-RAY DIFFRACTION100
2.3833-2.53260.25411400.20852663X-RAY DIFFRACTION100
2.5326-2.72810.25831400.22212666X-RAY DIFFRACTION100
2.7281-3.00260.26171420.21882692X-RAY DIFFRACTION100
3.0026-3.4370.23231420.20572703X-RAY DIFFRACTION100
3.437-4.32980.21521440.16982738X-RAY DIFFRACTION100
4.3298-47.6220.19271510.17552859X-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)
12.1381-0.9070.04563.0162-0.77492.1860.1371-0.0392-0.2721-0.0667-0.1383-0.00340.46120.16710.00770.29930.0041-0.02670.23810.0020.2655.44778.3454-8.1981
22.2122-0.7310.36432.8776-0.57881.03610.20880.09320.1464-0.2015-0.3073-0.28820.19570.13770.14150.24940.0337-0.00040.23280.01960.20936.905517.2851-10.7239
31.5592-1.4507-0.57454.27760.97681.1018-0.10940.0971-0.09170.2808-0.06890.2860.0328-0.25390.13160.2477-0.0421-0.00750.3485-0.06840.2818-14.68861.6591-19.3159
41.7429-2.81750.03724.60390.1520.7115-0.07980.0474-0.15820.326-0.12680.31690.0284-0.18870.2270.2776-0.06790.0170.344-0.10970.3161-13.1706-7.3629-21.5951
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 9 through 148 )
2X-RAY DIFFRACTION2chain 'A' and (resid 156 through 191 )
3X-RAY DIFFRACTION3chain 'O' and (resid 6 through 152 )
4X-RAY DIFFRACTION4chain 'O' and (resid 154 through 190 )

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