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- PDB-6p0x: Structure of the N-terminal domain of effector protein SpvB from ... -

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Basic information

Entry
Database: PDB / ID: 6p0x
TitleStructure of the N-terminal domain of effector protein SpvB from Salmonella typhimurium strain LT2
ComponentsSalmonella plasmid virulence: SpvB
KeywordsUNKNOWN FUNCTION / salmonella effector / SpvB / ADP-ribosyltransferase
Function / homology
Function and homology information


NAD+-protein-arginine ADP-ribosyltransferase activity => GO:0106274 / NAD+-protein-arginine ADP-ribosyltransferase / NAD+-protein-arginine ADP-ribosyltransferase activity / : / nucleotidyltransferase activity / toxin activity / extracellular region / cytoplasm
Similarity search - Function
Salmonella virulence plasmid 65kDa B protein / Salmonella virulence plasmid 65kDa B protein / ADP ribosyltransferase / ADP-ribosyltransferase exoenzyme
Similarity search - Domain/homology
ACRYLIC ACID / Mono(ADP-ribosyl)transferase SpvB
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsXu, C. / Boniecki, M. / Cygler, M.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)48370 Canada
CitationJournal: To Be Published
Title: Structure of the N-terminal domain of effector protein SpvB from Salmonella typhimurium strain LT2
Authors: Xu, C. / Boniecki, M. / Cygler, M.
History
DepositionMay 17, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2019Provider: 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 11, 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: Salmonella plasmid virulence: SpvB
B: Salmonella plasmid virulence: SpvB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,60715
Polymers73,3532
Non-polymers1,25413
Water4,774265
1
A: Salmonella plasmid virulence: SpvB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3539
Polymers36,6761
Non-polymers6778
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Salmonella plasmid virulence: SpvB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2546
Polymers36,6761
Non-polymers5785
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)101.351, 101.351, 211.302
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-576-

HOH

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Components

#1: Protein Salmonella plasmid virulence: SpvB


Mass: 36676.379 Da / Num. of mol.: 2 / Fragment: residues 26-355
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: spvB, spvA, PSLT039 / Plasmid: pMCSG7 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): star / References: UniProt: H9L477
#2: Chemical ChemComp-AKR / ACRYLIC ACID / Acrylic acid


Mass: 72.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H4O2
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER / Bis-tris methane


Mass: 209.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 265 / 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: 3.82 Å3/Da / Density % sol: 67.83 % / Description: Rod shape
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M Bis-Tris pH 6.5, 14% poly(acrylic acid) 5100 sodium salt, 4% PEG3350, 1 mM DTT and 20 mM MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: May 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 44119 / % possible obs: 100 % / Redundancy: 14.7 % / Rpim(I) all: 0.019 / Net I/σ(I): 41.29
Reflection shellResolution: 2.4→2.44 Å / Num. unique obs: 2160 / Rpim(I) all: 0.222 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(1.15.2_3472)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IGL

4igl


Resolution: 2.4→49.28 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / Phase error: 21.35
RfactorNum. reflection% reflection
Rfree0.2148 2077 4.74 %
Rwork0.1874 --
obs0.1887 43821 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.4→49.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4973 0 83 265 5321
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035200
X-RAY DIFFRACTIONf_angle_d0.6227098
X-RAY DIFFRACTIONf_dihedral_angle_d15.5543012
X-RAY DIFFRACTIONf_chiral_restr0.044751
X-RAY DIFFRACTIONf_plane_restr0.004930
LS refinement shellResolution: 2.4→2.48 Å
RfactorNum. reflection% reflection
Rfree0.2864 136 -
Rwork0.2526 2539 -
obs-4131 95.36 %
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)
14.75410.0812-1.39253.94830.79391.7760.0797-0.36350.2931-0.02490.0284-0.20620.0220.1284-0.03050.3088-0.01560.05130.2586-0.01810.162960.73064.690420.475
23.45090.15870.64643.4563-0.34271.3418-0.12270.10540.5477-0.13490.1-0.2792-0.10130.21780.00660.2741-0.06320.07470.2283-0.04310.285877.58073.6956-1.0969
32.3580.0825-0.50351.4747-0.21982.7578-0.1833-0.5512-0.2560.25380.1055-0.19980.32330.31990.02650.3410.08880.04790.28180.030.255569.1316-7.353118.1714
43.03720.68071.05573.64812.34926.4264-0.1703-0.6928-0.38960.46610.26250.04160.6659-0.2442-0.1820.4490.05220.13840.41080.01210.248650.9838-4.153927.1762
53.8382-0.2389-0.05893.539-2.86652.35580.01840.027-0.0237-0.3697-0.10620.52950.1136-0.62130.06050.25240.1084-0.11570.4418-0.19670.313333.96572.256245.7849
62.0139-0.785-0.00071.4378-1.33071.5837-0.13170.6048-0.0812-0.8142-0.26430.5781-0.4047-0.9186-0.37450.81510.4183-0.42790.9551-0.32980.53525.003210.590221.3238
70.96-0.7106-0.86631.83060.49011.63090.02050.05830.2537-0.406-0.19490.1594-0.7514-0.2617-0.0140.38870.2153-0.11680.3679-0.15460.364137.029116.103240.9374
82.98351.1446-1.69144.6014-0.47586.5253-0.2433-0.78330.18370.36830.1723-0.29980.04620.6294-0.02040.22460.094-0.09930.4173-0.1150.254945.76193.10553.6942
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 34 through 76 )
2X-RAY DIFFRACTION2chain 'A' and (resid 77 through 153 )
3X-RAY DIFFRACTION3chain 'A' and (resid 154 through 333 )
4X-RAY DIFFRACTION4chain 'A' and (resid 334 through 353 )
5X-RAY DIFFRACTION5chain 'B' and (resid 34 through 76 )
6X-RAY DIFFRACTION6chain 'B' and (resid 77 through 153)
7X-RAY DIFFRACTION7chain 'B' and (resid 154 through 333)
8X-RAY DIFFRACTION8chain 'B' and (resid 334 through 353)

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