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- PDB-6drh: ADP-ribosyltransferase toxin/immunity pair -

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Basic information

Entry
Database: PDB / ID: 6drh
TitleADP-ribosyltransferase toxin/immunity pair
Components
  • ADP-ribosyl-(Dinitrogen reductase) hydrolase
  • PAAR repeat-containing protein
KeywordsTOXIN / Immunity / Type VI secretion / ADP-ribosyltransferase
Function / homology
Function and homology information


[protein ADP-ribosylarginine] hydrolase / ADP-ribosylarginine hydrolase activity / NAD+-protein-arginine ADP-ribosyltransferase / NAD+-protein-arginine ADP-ribosyltransferase activity / NAD+-protein poly-ADP-ribosyltransferase activity / nucleotidyltransferase activity / toxin activity / host cell cytoplasm / extracellular region / metal ion binding
Similarity search - Function
: / NAD:arginine ADP-ribosyltransferase, ART / NAD:arginine ADP-ribosyltransferase / : / PAAR motif / PAAR motif / ADP-ribosylation/Crystallin J1 / ADP-ribosylglycohydrolase / ADP-ribosylation/Crystallin J1 superfamily / : / Toxin-related mono-ADP-ribosyltransferase (TR mART) core domain profile.
Similarity search - Domain/homology
PHOSPHATE ION / NAD(+)--protein-arginine ADP-ribosyltransferase Tre1 / ADP-ribosylarginine hydrolase Tri1
Similarity search - Component
Biological speciesSerratia proteamaculans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.299 Å
AuthorsBosch, D.E. / Ting, S. / Allaire, M. / Mougous, J.D.
CitationJournal: Cell / Year: 2018
Title: Bifunctional Immunity Proteins Protect Bacteria against FtsZ-Targeting ADP-Ribosylating Toxins.
Authors: Ting, S.Y. / Bosch, D.E. / Mangiameli, S.M. / Radey, M.C. / Huang, S. / Park, Y.J. / Kelly, K.A. / Filip, S.K. / Goo, Y.A. / Eng, J.K. / Allaire, M. / Veesler, D. / Wiggins, P.A. / Peterson, S.B. / Mougous, J.D.
History
DepositionJun 11, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 28, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first
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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ADP-ribosyl-(Dinitrogen reductase) hydrolase
B: PAAR repeat-containing protein
C: ADP-ribosyl-(Dinitrogen reductase) hydrolase
D: PAAR repeat-containing protein
E: ADP-ribosyl-(Dinitrogen reductase) hydrolase
F: PAAR repeat-containing protein
G: ADP-ribosyl-(Dinitrogen reductase) hydrolase
H: PAAR repeat-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)247,66912
Polymers247,3608
Non-polymers3094
Water30,7161705
1
A: ADP-ribosyl-(Dinitrogen reductase) hydrolase
B: PAAR repeat-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,9353
Polymers61,8402
Non-polymers951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5360 Å2
ΔGint-30 kcal/mol
Surface area20000 Å2
MethodPISA
2
C: ADP-ribosyl-(Dinitrogen reductase) hydrolase
D: PAAR repeat-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,9594
Polymers61,8402
Non-polymers1192
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5450 Å2
ΔGint-43 kcal/mol
Surface area19850 Å2
MethodPISA
3
E: ADP-ribosyl-(Dinitrogen reductase) hydrolase
F: PAAR repeat-containing protein


Theoretical massNumber of molelcules
Total (without water)61,8402
Polymers61,8402
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5110 Å2
ΔGint-21 kcal/mol
Surface area19710 Å2
MethodPISA
4
G: ADP-ribosyl-(Dinitrogen reductase) hydrolase
H: PAAR repeat-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,9353
Polymers61,8402
Non-polymers951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5470 Å2
ΔGint-31 kcal/mol
Surface area19530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.169, 151.006, 196.904
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain B and (resid 24 through 25 or resid 27 through 166 or resid 168 through 192))
21(chain D and (resid 24 through 25 or resid 27 through 166 or resid 168 through 192))
31(chain F and (resid 24 through 25 or resid 27 through 166 or resid 168 through 192))
41(chain H and (resid 24 through 25 or resid 27 through 166 or resid 168 through 192))
12(chain A and (resid 3 through 12 or resid 14...
22(chain C and (resid 3 through 12 or resid 14...
32(chain E and (resid 3 through 12 or resid 14...
42(chain G and (resid 3 through 12 or resid 14...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111GLNGLNALAALA(chain B and (resid 24 through 25 or resid 27 through 166 or resid 168 through 192))BB24 - 2520 - 21
121VALVALTYRTYR(chain B and (resid 24 through 25 or resid 27 through 166 or resid 168 through 192))BB27 - 16623 - 162
131PROPROPROPRO(chain B and (resid 24 through 25 or resid 27 through 166 or resid 168 through 192))BB168 - 192164 - 188
211GLNGLNALAALA(chain D and (resid 24 through 25 or resid 27 through 166 or resid 168 through 192))DD24 - 2520 - 21
221VALVALTYRTYR(chain D and (resid 24 through 25 or resid 27 through 166 or resid 168 through 192))DD27 - 16623 - 162
231PROPROPROPRO(chain D and (resid 24 through 25 or resid 27 through 166 or resid 168 through 192))DD168 - 192164 - 188
311GLNGLNALAALA(chain F and (resid 24 through 25 or resid 27 through 166 or resid 168 through 192))FF24 - 2520 - 21
321VALVALTYRTYR(chain F and (resid 24 through 25 or resid 27 through 166 or resid 168 through 192))FF27 - 16623 - 162
331PROPROPROPRO(chain F and (resid 24 through 25 or resid 27 through 166 or resid 168 through 192))FF168 - 192164 - 188
411GLNGLNALAALA(chain H and (resid 24 through 25 or resid 27 through 166 or resid 168 through 192))HH24 - 2520 - 21
421VALVALTYRTYR(chain H and (resid 24 through 25 or resid 27 through 166 or resid 168 through 192))HH27 - 16623 - 162
431PROPROPROPRO(chain H and (resid 24 through 25 or resid 27 through 166 or resid 168 through 192))HH168 - 192164 - 188
112ASPASPGLNGLN(chain A and (resid 3 through 12 or resid 14...AA3 - 123 - 12
122TYRTYRALAALA(chain A and (resid 3 through 12 or resid 14...AA14 - 1514 - 15
132ARGARGLEULEU(chain A and (resid 3 through 12 or resid 14...AA17 - 2117 - 21
142PROPROGLYGLY(chain A and (resid 3 through 12 or resid 14...AA40 - 4640 - 46
152ILEILEPROPRO(chain A and (resid 3 through 12 or resid 14...AA2 - 372 - 37
162GLUGLUGLYGLY(chain A and (resid 3 through 12 or resid 14...AA48 - 13348 - 133
172ILEILEPHEPHE(chain A and (resid 3 through 12 or resid 14...AA2 - 3662 - 366
182PROPROARGARG(chain A and (resid 3 through 12 or resid 14...AA186 - 248186 - 248
192ILEILEPHEPHE(chain A and (resid 3 through 12 or resid 14...AA2 - 3662 - 366
1102ALAALAGLYGLY(chain A and (resid 3 through 12 or resid 14...AA251 - 269251 - 269
1112LYSLYSLYSLYS(chain A and (resid 3 through 12 or resid 14...AA274274
1122ARGARGPHEPHE(chain A and (resid 3 through 12 or resid 14...AA276 - 366276 - 366
212ASPASPGLNGLN(chain C and (resid 3 through 12 or resid 14...CC3 - 123 - 12
222TYRTYRALAALA(chain C and (resid 3 through 12 or resid 14...CC14 - 1514 - 15
232ARGARGLEULEU(chain C and (resid 3 through 12 or resid 14...CC17 - 2117 - 21
242PROPROSERSER(chain C and (resid 3 through 12 or resid 14...CC23 - 2623 - 26
252ILEILEPROPRO(chain C and (resid 3 through 12 or resid 14...CC2 - 372 - 37
262PROPROGLYGLY(chain C and (resid 3 through 12 or resid 14...CC40 - 4640 - 46
272ILEILEPHEPHE(chain C and (resid 3 through 12 or resid 14...CC2 - 3662 - 366
282ILEILEPHEPHE(chain C and (resid 3 through 12 or resid 14...CC2 - 3662 - 366
292ALAALAGLYGLY(chain C and (resid 3 through 12 or resid 14...CC251 - 269251 - 269
2102LYSLYSLYSLYS(chain C and (resid 3 through 12 or resid 14...CC274274
2112ARGARGPHEPHE(chain C and (resid 3 through 12 or resid 14...CC276 - 366276 - 366
312ASPASPGLNGLN(chain E and (resid 3 through 12 or resid 14...EE3 - 123 - 12
322TYRTYRALAALA(chain E and (resid 3 through 12 or resid 14...EE14 - 1514 - 15
332ARGARGLEULEU(chain E and (resid 3 through 12 or resid 14...EE17 - 2117 - 21
342PROPROGLYGLY(chain E and (resid 3 through 12 or resid 14...EE40 - 4640 - 46
352GLUGLUGLYGLY(chain E and (resid 3 through 12 or resid 14...EE48 - 13348 - 133
362METMETPHEPHE(chain E and (resid 3 through 12 or resid 14...EE1 - 3661 - 366
372PROPROARGARG(chain E and (resid 3 through 12 or resid 14...EE186 - 248186 - 248
382ALAALAGLYGLY(chain E and (resid 3 through 12 or resid 14...EE251 - 269251 - 269
392TYRTYRLYSLYS(chain E and (resid 3 through 12 or resid 14...EE271 - 272271 - 272
3102LYSLYSLYSLYS(chain E and (resid 3 through 12 or resid 14...EE274274
3112ARGARGPHEPHE(chain E and (resid 3 through 12 or resid 14...EE276 - 366276 - 366
412ASPASPGLNGLN(chain G and (resid 3 through 12 or resid 14...GG3 - 123 - 12
422TYRTYRALAALA(chain G and (resid 3 through 12 or resid 14...GG14 - 1514 - 15
432ARGARGLEULEU(chain G and (resid 3 through 12 or resid 14...GG17 - 2117 - 21
442PROPROSERSER(chain G and (resid 3 through 12 or resid 14...GG23 - 2623 - 26
452ILEILEPROPRO(chain G and (resid 3 through 12 or resid 14...GG2 - 372 - 37
462PROPROGLYGLY(chain G and (resid 3 through 12 or resid 14...GG40 - 4640 - 46
472ILEILEPHEPHE(chain G and (resid 3 through 12 or resid 14...GG2 - 3662 - 366
482ILEILEPHEPHE(chain G and (resid 3 through 12 or resid 14...GG2 - 3662 - 366
492ALAALAGLYGLY(chain G and (resid 3 through 12 or resid 14...GG251 - 269251 - 269
4102LYSLYSLYSLYS(chain G and (resid 3 through 12 or resid 14...GG274274
4112ARGARGPHEPHE(chain G and (resid 3 through 12 or resid 14...GG276 - 366276 - 366

NCS ensembles :
ID
1
2

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Components

#1: Protein
ADP-ribosyl-(Dinitrogen reductase) hydrolase


Mass: 40977.055 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia proteamaculans (strain 568) (bacteria)
Strain: 568 / Gene: Spro_3018 / Production host: Escherichia coli (E. coli)
References: UniProt: A8GG79, ADP-ribosyl-[dinitrogen reductase] hydrolase
#2: Protein
PAAR repeat-containing protein


Mass: 20862.826 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia proteamaculans (strain 568) (bacteria)
Strain: 568 / Gene: Spro_3017 / Production host: Escherichia coli (E. coli) / References: UniProt: A8GG78
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1705 / 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: 2.64 Å3/Da / Density % sol: 53.36 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Na2HPO4, 1.6 M citric acid pH 4.2 / Temp details: 298

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Sep 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.299→50 Å / Num. obs: 115805 / % possible obs: 99.8 % / Redundancy: 5.1 % / Biso Wilson estimate: 24.55 Å2 / Rmerge(I) obs: 0.119 / Net I/σ(I): 9
Reflection shellResolution: 2.3→2.32 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.492 / Mean I/σ(I) obs: 2 / Num. unique obs: 2853 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
SCALEPACKdata scaling
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6DRE

6dre


Resolution: 2.299→49.535 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 19.48
RfactorNum. reflection% reflection
Rfree0.2064 1999 1.73 %
Rwork0.1516 --
obs0.1525 115662 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 111.15 Å2 / Biso mean: 27.5344 Å2 / Biso min: 8.99 Å2
Refinement stepCycle: final / Resolution: 2.299→49.535 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17207 0 16 1705 18928
Biso mean--41.63 32.21 -
Num. residues----2194
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01517622
X-RAY DIFFRACTIONf_angle_d1.41223942
X-RAY DIFFRACTIONf_chiral_restr0.072596
X-RAY DIFFRACTIONf_plane_restr0.0093173
X-RAY DIFFRACTIONf_dihedral_angle_d3.8211941
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11B3156X-RAY DIFFRACTION6.313TORSIONAL
12D3156X-RAY DIFFRACTION6.313TORSIONAL
13F3156X-RAY DIFFRACTION6.313TORSIONAL
14H3156X-RAY DIFFRACTION6.313TORSIONAL
21A6658X-RAY DIFFRACTION6.313TORSIONAL
22C6658X-RAY DIFFRACTION6.313TORSIONAL
23E6658X-RAY DIFFRACTION6.313TORSIONAL
24G6658X-RAY DIFFRACTION6.313TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2989-2.35640.24971390.17977931807098
2.3564-2.42010.29391420.182980068148100
2.4201-2.49130.23731400.183180258165100
2.4913-2.57170.26961410.17647993813499
2.5717-2.66360.22811420.173780428184100
2.6636-2.77030.24931420.171780918233100
2.7703-2.89630.22331410.173180778218100
2.8963-3.0490.29411430.177680678210100
3.049-3.240.22881430.165581308273100
3.24-3.49010.19951430.149481468289100
3.4901-3.84120.1631440.131381468290100
3.8412-4.39670.14811430.112582098352100
4.3967-5.53820.17911470.120882588405100
5.5382-49.54630.17181490.15285428691100

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