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- PDB-4xzj: Crystal structure of ADP-ribosyltransferase Vis in complex with NAD -

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Basic information

Entry
Database: PDB / ID: 4xzj
TitleCrystal structure of ADP-ribosyltransferase Vis in complex with NAD
ComponentsPutative NAD(+)--arginine ADP-ribosyltransferase Vis
KeywordsTRANSFERASE
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
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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Putative NAD(+)--arginine ADP-ribosyltransferase Vis
Similarity search - Component
Biological speciesVibrio splendidus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsPfoh, R. / Ravulapalli, R. / Merrill, A.R. / Pai, E.F.
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 4, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2015Group: Database references
Revision 1.2Oct 28, 2015Group: Database references
Revision 1.3Nov 22, 2017Group: Database references / Derived calculations / Refinement description
Category: citation / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.4Sep 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)27,7002
Polymers27,0371
Non-polymers6631
Water2,612145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.700, 52.000, 100.400
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Detailsbiological unit is the same as asym.

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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 / Plasmid: pet 28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A3UNN4, NAD+-protein-arginine ADP-ribosyltransferase
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / 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: 2.61 Å3/Da / Density % sol: 52.8 %
Crystal growTemperature: 298 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: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 29, 2011
RadiationMonochromator: multi-layer / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. obs: 23562 / % possible obs: 94.7 % / Redundancy: 6.25 % / Rmerge(I) obs: 0.0445 / Net I/σ(I): 25.84
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 5.24 % / Rmerge(I) obs: 0.1799 / Mean I/σ(I) obs: 8.67 / % possible all: 91.8

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Processing

Software
NameVersionClassification
XDSdata reduction
PDB_EXTRACT3.14data extraction
REFMAC5.7.0029refinement
SHELXphasing
PHASER2.5.1phasing
XPREPdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Y1W

4y1w


Resolution: 1.8→18.63 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.946 / WRfactor Rfree: 0.2105 / WRfactor Rwork: 0.1802 / FOM work R set: 0.8824 / SU B: 4.226 / SU ML: 0.069 / SU R Cruickshank DPI: 0.1222 / SU Rfree: 0.1147 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.122 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2054 1191 5.1 %RANDOM
Rwork0.1751 22333 --
obs0.1767 23524 94.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 66.56 Å2 / Biso mean: 23.386 Å2 / Biso min: 13.86 Å2
Baniso -1Baniso -2Baniso -3
1--0.47 Å20 Å20 Å2
2--1 Å20 Å2
3----0.53 Å2
Refinement stepCycle: final / Resolution: 1.8→18.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1756 0 44 145 1945
Biso mean--18.38 27.47 -
Num. residues----222
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0191913
X-RAY DIFFRACTIONr_bond_other_d0.0010.021773
X-RAY DIFFRACTIONr_angle_refined_deg1.4241.9732619
X-RAY DIFFRACTIONr_angle_other_deg0.76834100
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8325243
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.0624.45792
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.92715324
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9981512
X-RAY DIFFRACTIONr_chiral_restr0.0890.2289
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022184
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02453
LS refinement shellResolution: 1.8→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.241 82 -
Rwork0.212 1551 -
all-1633 -
obs--91.38 %
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)
10.6722-0.0484-0.00080.04620.08540.3666-0.0584-0.05870.0637-0.0330.02620.0057-0.04740.04880.03220.0418-0.0113-0.01340.01570.00260.02229.343347.5198.1599
20.40030.01710.080.3233-0.08630.4468-0.018-0.00260.0015-0.02680.0020.00110.0189-0.00640.0160.02740.00060.00590.0002-0.0010.01370.984336.903113.1626
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A19 - 109
2X-RAY DIFFRACTION2A110 - 700

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