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- PDB-4yc0: Crystal structure of ADP-ribosyltransferase Vis in complex with M... -

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Basic information

Entry
Database: PDB / ID: 4yc0
TitleCrystal structure of ADP-ribosyltransferase Vis in complex with M6 Inhibitor
ComponentsPutative NAD(+)--arginine ADP-ribosyltransferase Vis
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Inhibitor / Transferase / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


NAD+-protein-arginine ADP-ribosyltransferase / NAD+-protein-arginine ADP-ribosyltransferase activity / nucleotidyltransferase activity / toxin activity / nucleotide binding / extracellular region
Similarity search - Function
ADP ribosyltransferase / ADP-ribosyltransferase exoenzyme / Toxin-related mono-ADP-ribosyltransferase (TR mART) core domain profile.
Similarity search - Domain/homology
Chem-5OF / Putative NAD(+)--arginine ADP-ribosyltransferase Vis
Similarity search - Component
Biological speciesVibrio splendidus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsRavulapalli, R. / Merrill, A.R.
CitationJournal: Biochemistry / Year: 2015
Title: Characterization of Vis Toxin, a Novel ADP-Ribosyltransferase from Vibrio splendidus.
Authors: Ravulapalli, R. / Lugo, M.R. / Pfoh, R. / Visschedyk, D. / Poole, A. / Fieldhouse, R.J. / Pai, E.F. / Merrill, A.R.
History
DepositionFeb 19, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Derived calculations / Structure summary / Category: audit_author / pdbx_struct_oper_list
Item: _audit_author.name / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 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

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Assembly

Deposited unit
A: Putative NAD(+)--arginine ADP-ribosyltransferase Vis
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2412
Polymers27,0371
Non-polymers2041
Water5,639313
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.230, 52.160, 101.600
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 Putative NAD(+)--arginine ADP-ribosyltransferase Vis / Putative mono(ADP-ribosyl)transferase / mART / Toxin Vis


Mass: 27037.045 Da / Num. of mol.: 1 / Fragment: residues 20-240
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio splendidus (bacteria) / Gene: V12B01_18061 / Production host: Escherichia coli (E. coli)
References: UniProt: A3UNN4, NAD+-protein-arginine ADP-ribosyltransferase
#2: Chemical ChemComp-5OF / 2-(4-oxidanylidene-3~{H}-phthalazin-1-yl)ethanoic acid


Mass: 204.182 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H8N2O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 313 / 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: 2.36 Å3/Da / Density % sol: 47.96 %
Crystal growTemperature: 297.15 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 30% Jeffamine ED-2001, 0.1 M Hepes

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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: Dec 12, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.5→46.4 Å / Num. obs: 69774 / % possible obs: 99.98 % / Redundancy: 7.2 % / Rsym value: 0.09 / Net I/σ(I): 13.04
Reflection shellResolution: 1.5→1.554 Å / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Y1W

4y1w


Resolution: 1.5→46.4 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 16.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1803 2092 5 %
Rwork0.1581 --
obs0.1593 41825 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.5→46.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1759 0 15 313 2087
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081819
X-RAY DIFFRACTIONf_angle_d0.9272468
X-RAY DIFFRACTIONf_dihedral_angle_d13.3791083
X-RAY DIFFRACTIONf_chiral_restr0.051269
X-RAY DIFFRACTIONf_plane_restr0.006319
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.53490.22891370.20412606X-RAY DIFFRACTION100
1.5349-1.57330.20161370.18832603X-RAY DIFFRACTION100
1.5733-1.61580.21341380.17482616X-RAY DIFFRACTION100
1.6158-1.66340.18791380.16622618X-RAY DIFFRACTION100
1.6634-1.71710.18231360.17152594X-RAY DIFFRACTION100
1.7171-1.77840.19531390.16892637X-RAY DIFFRACTION100
1.7784-1.84970.2031380.16432621X-RAY DIFFRACTION100
1.8497-1.93380.17581390.15912630X-RAY DIFFRACTION100
1.9338-2.03580.16711380.14992624X-RAY DIFFRACTION100
2.0358-2.16330.18041390.14642649X-RAY DIFFRACTION100
2.1633-2.33040.19351390.15422639X-RAY DIFFRACTION100
2.3304-2.56490.17561410.14512671X-RAY DIFFRACTION100
2.5649-2.9360.18411400.15592667X-RAY DIFFRACTION100
2.936-3.69880.16861430.15342720X-RAY DIFFRACTION100
3.6988-46.42440.17161500.15992838X-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)
10.55790.2569-0.14660.12390.13380.3062-0.08320.0017-0.22750.09210.01650.23610.1016-0.1714-0.00330.13340.00520.03730.14770.03840.1951-7.2031-25.4298-6.0365
21.02220.06540.30840.31560.05881.10660.0572-0.0645-0.1880.0699-0.0448-0.13260.03940.170.02990.07860.0235-0.0070.13350.02040.146517.646-19.5056-8.9493
30.6777-0.02110.16530.0994-0.21470.8341-0.03040.00730.00180.0477-0.01370.0252-0.108-0.0323-0.03530.10980.0123-0.01610.0876-0.01420.0865-0.1305-11.7274-12.6777
40.75180.2149-0.01440.5209-0.37551.0303-0.0053-0.05930.03020.050.03180.0132-0.0779-0.005200.10380.0069-0.01550.0978-0.00650.0768-0.0939-12.2595-11.4653
50.1938-0.2663-0.05150.1466-0.01590.2308-0.22170.15520.0529-0.0035-0.1213-0.4386-0.08530.4928-0.07020.19120.001-0.04470.13430.03960.17466.8337-3.6494-23.5592
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 19 through 48 )
2X-RAY DIFFRACTION2chain 'A' and (resid 49 through 107 )
3X-RAY DIFFRACTION3chain 'A' and (resid 108 through 153 )
4X-RAY DIFFRACTION4chain 'A' and (resid 154 through 219 )
5X-RAY DIFFRACTION5chain 'A' and (resid 220 through 240 )

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