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

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Basic information

Entry
Database: PDB / ID: 6dre
TitleADP-ribosyltransferase toxin/immunity pair
Components
  • ADP-ribosyl-(Dinitrogen reductase) hydrolase
  • PAAR repeat-containing protein
KeywordsTOXIN / Immunity / Type VI secretion / ADP ribosyl transferase
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+ 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 / : / ADP-ribosylglycohydrolase fold / ADP-ribosylation/Crystallin J1 / PAAR motif / PAAR motif / ADP-ribosylation/Crystallin J1 / ADP-ribosylglycohydrolase ...: / NAD:arginine ADP-ribosyltransferase, ART / NAD:arginine ADP-ribosyltransferase / : / ADP-ribosylglycohydrolase fold / ADP-ribosylation/Crystallin J1 / 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. / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
NAD(+)--protein-arginine ADP-ribosyltransferase Tre1 / ADP-ribosylarginine hydrolase Tri1
Similarity search - Component
Biological speciesSerratia proteamaculans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 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 1.2Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,2823
Polymers60,2582
Non-polymers241
Water10,791599
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5240 Å2
ΔGint-31 kcal/mol
Surface area19400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.355, 51.036, 94.899
Angle α, β, γ (deg.)90.000, 123.710, 90.000
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 41399.109 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia proteamaculans (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: 18858.576 Da / Num. of mol.: 1
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-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 599 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.29 Å3/Da / Density % sol: 46.36 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.2 / Details: 0.1 M Na2HPO4, 1.6 M citric acid pH 4.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9794 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Sep 5, 2017
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.8→67 Å / Num. obs: 95211 / % possible obs: 97.3 % / Redundancy: 6.4 % / Biso Wilson estimate: 18.1 Å2 / Rmerge(I) obs: 0.045 / Net I/av σ(I): 33.2 / Net I/σ(I): 33.2
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.391 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1081 / % possible all: 93

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MAD / Resolution: 1.8→66.899 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.18
RfactorNum. reflection% reflection
Rfree0.1946 3866 4.06 %
Rwork0.1509 --
obs0.1527 95211 96.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 88.52 Å2 / Biso mean: 24.8286 Å2 / Biso min: 10.07 Å2
Refinement stepCycle: final / Resolution: 1.8→66.899 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4185 0 1 599 4785
Biso mean--22.73 34.21 -
Num. residues----535
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014284
X-RAY DIFFRACTIONf_angle_d1.0815822
X-RAY DIFFRACTIONf_chiral_restr0.061636
X-RAY DIFFRACTIONf_plane_restr0.007771
X-RAY DIFFRACTIONf_dihedral_angle_d2.8753265
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 28

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.8220.28281330.22313165329893
1.822-1.8450.23651340.2063094322894
1.845-1.86930.19431350.19433260339595
1.8693-1.89490.28171380.20673192333095
1.8949-1.9220.24361360.19283235337195
1.922-1.95070.23131360.18413202333895
1.9507-1.98120.22671380.17223249338796
1.9812-2.01370.20581380.17663258339696
2.0137-2.04840.20151380.16173233337196
2.0484-2.08560.21781360.15543209334596
2.0856-2.12580.19391380.15153288342696
2.1258-2.16920.22291360.14423213334996
2.1692-2.21630.21941400.14723332347296
2.2163-2.26790.18561370.15433183332096
2.2679-2.32460.23471370.16313278341596
2.3246-2.38750.20661340.15253235336997
2.3875-2.45770.2371370.15863272340997
2.4577-2.5370.22261380.15423302344097
2.537-2.62770.2121400.15013284342497
2.6277-2.73290.19011370.15623267340497
2.7329-2.85730.18351400.15833281342197
2.8573-3.0080.22971440.16513368351298
3.008-3.19640.211380.16143271340998
3.1964-3.44320.17051400.1433299343998
3.4432-3.78970.18691400.12993320346099
3.7897-4.3380.15511430.11833348349199
4.338-5.4650.13781400.12133346348699
5.465-66.94480.16591450.1483361350699
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)
11.62871.159-1.62433.35331.77587.38090.19020.03530.1896-0.0933-0.10360.2146-0.6733-0.8956-0.07470.21080.06390.00890.2920.00150.193830.160250.380827.264
23.58521.8256-4.73183.9558-2.04446.27440.08240.12470.1947-0.0048-0.02220.3128-0.1742-0.3599-0.02230.1983-0.0198-0.01940.3383-0.0460.219713.014436.398118.9549
30.9054-0.0394-0.40410.1643-0.02691.4772-0.05890.37650.0303-0.04680.0039-0.0081-0.0265-0.10820.04630.1792-0.0153-00.060.02770.15939.092338.13698.7787
42.5223-0.8999-1.13113.4092.24532.9387-0.1254-0.1956-0.01380.05890.1712-0.0908-0.00560.337-0.05770.1049-0.023-0.02060.19930.04340.153163.908341.334226.2242
51.79540.1030.27011.8055-0.07933.8930.0988-0.0932-0.45830.0583-0.0314-0.20970.39930.069-0.03550.1792-0.00510.010.08730.04160.219650.156122.112418.5943
66.16272.9623-4.01013.2965-1.193.77770.0614-0.8976-0.52040.2555-0.1705-0.09560.12320.45610.10620.20270.0069-0.03570.25880.11570.218652.899822.967328.4014
70.98390.10590.03720.34670.04971.1891-0.0180.03330.052-0.0389-0.0278-0.0083-0.0392-0.00980.0490.133-0.02-0.0030.0940.02060.138945.958939.31216.1057
87.76815.02180.77277.9584-0.21453.1151-0.08860.3208-0.4153-0.16140.086-0.05630.3087-0.2920.00290.2045-0.05730.01160.1886-0.0590.123122.849917.953312.6505
92.390.0761-1.36232.3064-0.04891.2343-0.0362-0.0553-0.40510.0398-0.0930.02710.2395-0.15740.14030.1903-0.0678-0.00040.2003-0.02660.149124.672818.528320.125
109.45762.5454-7.69453.7064-3.47138.4707-0.00290.21530.1606-0.02470.11430.13270.1052-0.2911-0.11010.1365-0.0701-0.02940.2106-0.01110.16927.076324.834924.4955
112.02750.1559-0.20722.829-0.5371.035-0.0437-0.1459-0.19670.10640.0053-0.04160.1026-0.06280.06040.1554-0.04460.02660.2507-0.01070.120.047724.887127.8103
127.85040.89356.25830.45420.81835.0295-0.152-0.59590.1098-0.0175-0.14870.5612-0.1677-1.13250.24030.16730.02120.00240.3756-0.05830.3188.762943.767436.1437
130.2157-0.1356-0.76220.07390.44512.62170.2706-0.39060.22040.2626-0.35670.1587-0.3365-0.03450.02260.2723-0.10880.01330.3312-0.08470.203515.688232.393731.4663
141.1975-0.8144-1.28532.1872.25093.4833-0.0714-0.00550.0683-0.08760.01470.0576-0.0792-0.07460.04760.0918-0.0379-0.0190.1711-0.02060.13521.749335.43626.858
157.0137-1.471.79263.7854-4.92686.4902-0.20440.20630.45960.10160.08650.0191-0.37780.11950.11970.2467-0.0124-0.05180.2408-0.06350.15219.260744.441433.8723
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 21 )A2 - 21
2X-RAY DIFFRACTION2chain 'A' and (resid 22 through 39 )A22 - 39
3X-RAY DIFFRACTION3chain 'A' and (resid 40 through 89 )A40 - 89
4X-RAY DIFFRACTION4chain 'A' and (resid 90 through 116 )A90 - 116
5X-RAY DIFFRACTION5chain 'A' and (resid 117 through 150 )A117 - 150
6X-RAY DIFFRACTION6chain 'A' and (resid 151 through 176 )A151 - 176
7X-RAY DIFFRACTION7chain 'A' and (resid 177 through 366 )A177 - 366
8X-RAY DIFFRACTION8chain 'B' and (resid 4 through 19 )B4 - 19
9X-RAY DIFFRACTION9chain 'B' and (resid 20 through 39 )B20 - 39
10X-RAY DIFFRACTION10chain 'B' and (resid 40 through 58 )B40 - 58
11X-RAY DIFFRACTION11chain 'B' and (resid 59 through 86 )B59 - 86
12X-RAY DIFFRACTION12chain 'B' and (resid 87 through 100 )B87 - 100
13X-RAY DIFFRACTION13chain 'B' and (resid 101 through 111 )B101 - 111
14X-RAY DIFFRACTION14chain 'B' and (resid 112 through 158 )B112 - 158
15X-RAY DIFFRACTION15chain 'B' and (resid 159 through 172 )B159 - 172

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