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- PDB-5ewy: Scabin toxin from Streptomyces Scabies in complex with inhibitor P6E -

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Basic information

Entry
Database: PDB / ID: 5ewy
TitleScabin toxin from Streptomyces Scabies in complex with inhibitor P6E
ComponentsPutative ADP-Ribosyltransferase Scabin
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / transferase / inhibitor / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology: / nucleotide binding / Chem-5TQ / Putative secreted protein
Function and homology information
Biological speciesStreptomyces scabiei 87.22 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.4 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 22, 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

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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)22,2972
Polymers21,9931
Non-polymers3041
Water3,333185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.170, 60.530, 37.940
Angle α, β, γ (deg.)90.00, 100.25, 90.00
Int Tables number5
Space group name H-MC121

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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-5TQ / 4-(8-fluoranyl-6-oxidanylidene-1,3,4,5-tetrahydrobenzo[c][1,6]naphthyridin-2-yl)butanoic acid


Mass: 304.316 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H17FN2O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 45.07 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / Details: 0.1 M MES, pH 6.5, 15% w/v PEG400

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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: 1.4→49.456 Å / Num. obs: 38076 / % possible obs: 100 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.029 / Net I/σ(I): 20.44
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.72 / Mean I/σ(I) obs: 1.69 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata scaling
RefinementResolution: 1.4→42.889 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 18.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1655 1903 5 %
Rwork0.1528 --
obs0.1534 38050 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.4→42.889 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1315 0 22 185 1522
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081397
X-RAY DIFFRACTIONf_angle_d1.0141918
X-RAY DIFFRACTIONf_dihedral_angle_d17.226510
X-RAY DIFFRACTIONf_chiral_restr0.079195
X-RAY DIFFRACTIONf_plane_restr0.007252
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.4350.30521320.33242511X-RAY DIFFRACTION98
1.435-1.47380.26911370.26242603X-RAY DIFFRACTION99
1.4738-1.51720.25271360.22552583X-RAY DIFFRACTION100
1.5172-1.56620.21661330.20932521X-RAY DIFFRACTION100
1.5662-1.62220.21771360.18732583X-RAY DIFFRACTION100
1.6222-1.68710.21111350.17642568X-RAY DIFFRACTION100
1.6871-1.76390.17811360.16462593X-RAY DIFFRACTION100
1.7639-1.85690.1771350.15432556X-RAY DIFFRACTION100
1.8569-1.97320.14491380.14582617X-RAY DIFFRACTION100
1.9732-2.12560.21021350.14772579X-RAY DIFFRACTION100
2.1256-2.33950.171370.14762596X-RAY DIFFRACTION100
2.3395-2.6780.15881370.14592597X-RAY DIFFRACTION99
2.678-3.37370.17191360.14322598X-RAY DIFFRACTION99
3.3737-42.90940.12731400.13662642X-RAY DIFFRACTION99
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)
12.27732.50812.00093.2711.71832.21120.67740.55390.33160.1376-0.183-0.402-0.33430.343-0.14250.4640.05540.0920.5690.0510.38242.70438.42512.5186
22.4924-0.6403-0.52381.67490.23581.53470.04310.63660.1511-0.26170.00190.2276-0.0457-0.5048-0.02680.1914-0.0026-0.03360.33520.04350.18424.283633.95748.7965
34.5579-2.5978-0.34724.26260.31642.1854-0.17540.30060.00780.08070.08720.6273-0.1234-0.59860.12590.17450.01750.00830.3040.04460.244517.09536.992215.3953
42.1861-0.82010.08175.3088-2.87325.3034-0.1123-0.13710.02760.16330.1103-0.03310.1349-0.19190.03370.17360.0031-0.01460.1571-0.02380.149134.444833.522923.6489
53.6635-0.3336-0.99474.1999-0.89511.4586-0.0576-0.0444-0.03950.30910.0370.2215-0.0389-0.15970.01090.1698-0.0286-0.00470.1591-0.01610.126129.547930.038518.6916
62.8585-0.9304-0.42734.9424-2.76832.38730.0418-0.21340.57120.81770.10610.2655-1.1971-0.1897-0.2060.39660.07260.05240.19380.01480.333826.718747.57920.6328
73.0046-1.2292-0.80134.7513-0.30151.0733-0.01790.30050.01-0.05030.01280.17880.0574-0.247-0.01540.129-0.02750.00940.1721-0.00050.114528.897731.819113.4693
82.2149-0.06870.60732.7514-0.70125.2255-0.0904-0.0388-0.19120.0868-0.0030.03890.397-0.44770.08770.1613-0.01690.03420.1201-0.01090.16435.428422.70118.0099
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 89 )
3X-RAY DIFFRACTION3chain 'A' and (resid 90 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 200 )

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