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- PDB-5ewk: Scabin toxin from Streptomyces Scabies in complex with inhibitor PJ34 -

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Basic information

Entry
Database: PDB / ID: 5ewk
TitleScabin toxin from Streptomyces Scabies in complex with inhibitor PJ34
ComponentsPutative ADP-Ribosyltransferase Scabin
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / transferase / inhibitor / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology: / Scabin-like / nucleotide binding / Chem-P34 / Putative secreted protein
Function and homology information
Biological speciesStreptomyces scabiei 87.22 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsRavulapalli, R. / Lyons, B. / Merrill, A.R.
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Scabin, a Novel DNA-acting ADP-ribosyltransferase from Streptomyces scabies.
Authors: Lyons, B. / Ravulapalli, R. / Lanoue, J. / Lugo, M.R. / Dutta, D. / Carlin, S. / Merrill, A.R.
History
DepositionNov 20, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 6, 2016Group: Database references
Revision 1.2Jun 8, 2016Group: Database references
Revision 1.3Nov 22, 2017Group: Advisory / Database references ...Advisory / Database references / Derived calculations / Refinement description
Category: citation / pdbx_struct_oper_list ...citation / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms / software
Item: _citation.journal_id_CSD / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.4Sep 27, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative ADP-Ribosyltransferase Scabin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2882
Polymers21,9931
Non-polymers2951
Water2,576143
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area720 Å2
ΔGint-3 kcal/mol
Surface area8990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.470, 61.180, 38.030
Angle α, β, γ (deg.)90.00, 100.38, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-433-

HOH

21A-479-

HOH

31A-523-

HOH

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Components

#1: Protein Putative ADP-Ribosyltransferase Scabin


Mass: 21992.600 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces scabiei 87.22 (bacteria) / Strain: 87.22 / Gene: SCAB_27771 / Production host: Escherichia coli (E. coli)
References: UniProt: C9Z6T8, NAD+-protein-arginine ADP-ribosyltransferase
#2: Chemical ChemComp-P34 / N~2~,N~2~-DIMETHYL-N~1~-(6-OXO-5,6-DIHYDROPHENANTHRIDIN-2-YL)GLYCINAMIDE


Mass: 295.336 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H17N3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / 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

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Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 45.95 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / Details: 0.1 M MES, pH 6.5, 15% w/v PEG400 / PH range: 6.5

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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: Jul 15, 2015
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.6→37.41 Å / Num. all: 26086 / Num. obs: 26018 / % possible obs: 100 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.029 / Rsym value: 0.02 / Net I/σ(I): 23.33
Reflection shellResolution: 1.6→1.657 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2.56 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5DAZ

5daz


Resolution: 1.6→37.41 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.179 1300 5 %
Rwork0.1536 --
obs0.1549 25993 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→37.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1315 0 22 143 1480
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091397
X-RAY DIFFRACTIONf_angle_d1.0491918
X-RAY DIFFRACTIONf_dihedral_angle_d14.129819
X-RAY DIFFRACTIONf_chiral_restr0.06195
X-RAY DIFFRACTIONf_plane_restr0.007252
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.66410.25361430.24332721X-RAY DIFFRACTION100
1.6641-1.73980.23861440.21272730X-RAY DIFFRACTION100
1.7398-1.83150.22741440.18452726X-RAY DIFFRACTION100
1.8315-1.94630.18751420.15912724X-RAY DIFFRACTION100
1.9463-2.09660.18861440.15942730X-RAY DIFFRACTION99
2.0966-2.30750.2141450.15822745X-RAY DIFFRACTION100
2.3075-2.64140.17061450.15512759X-RAY DIFFRACTION100
2.6414-3.32770.17941450.15382749X-RAY DIFFRACTION100
3.3277-43.03490.15311480.13422809X-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)
15.84252.80487.20352.41953.11688.99140.41471.20860.1563-0.0684-0.0195-0.1486-0.49730.8222-0.42380.53410.09490.16030.64740.04330.414242.592238.4322.6657
23.0172-0.9768-0.50152.12950.34491.94010.06460.6890.033-0.3575-0.09040.3298-0.0445-0.59070.00670.22980.0005-0.05070.39330.01120.200522.122434.13879.5777
36.0056-2.26290.1663.28861.93231.8694-0.1881-0.05990.25920.08760.05140.3556-0.2797-0.66720.17840.25620.0643-0.00740.34860.04320.241119.005239.11518.0426
43.9862-2.00841.08556.9162-3.41283.7498-0.2144-0.22170.01570.31250.1888-0.06180.0414-0.20690.08420.20860.0139-0.01860.1893-0.02950.155534.545933.472223.6932
53.5273-0.4968-0.08933.4027-0.10240.01-0.0141-0.0825-0.17140.37290.0430.3876-0.0791-0.2368-0.01630.2435-0.0220.04110.20920.00040.166229.588529.96318.725
63.0672-1.0981-2.00396.4196-2.85053.42290.1267-0.19940.60020.74350.0005-0.1114-1.23230.1198-0.11970.40090.0429-0.00040.25640.00190.353426.838147.520320.7308
73.3081-1.6169-0.52945.3124-0.54131.9908-0.00120.3571-0.0911-0.1611-0.06280.16630.0912-0.33080.05330.1324-0.03550.01430.1873-0.01030.103928.90731.817513.4865
84.15291.01573.18122.61990.59166.817-0.1038-0.7964-0.23540.571-0.04770.13680.244-0.72020.10820.38650.01930.08430.27560.07470.245435.733921.958428.7884
94.1436-0.16981.23328.4552-2.17494.8426-0.07680.588-0.2793-0.9042-0.01930.12720.5648-0.35110.16510.2314-0.02530.04410.2403-0.08450.199635.135823.45626.6345
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 36 through 45 )
2X-RAY DIFFRACTION2chain 'A' and (resid 46 through 102 )
3X-RAY DIFFRACTION3chain 'A' and (resid 103 through 119 )
4X-RAY DIFFRACTION4chain 'A' and (resid 120 through 127 )
5X-RAY DIFFRACTION5chain 'A' and (resid 128 through 144 )
6X-RAY DIFFRACTION6chain 'A' and (resid 145 through 155 )
7X-RAY DIFFRACTION7chain 'A' and (resid 156 through 177 )
8X-RAY DIFFRACTION8chain 'A' and (resid 178 through 189 )
9X-RAY DIFFRACTION9chain 'A' and (resid 190 through 200 )

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