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- PDB-5daz: Crystal structure of Scabin, a mono-ADP-ribosyltransferase from S... -

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Basic information

Entry
Database: PDB / ID: 5daz
TitleCrystal structure of Scabin, a mono-ADP-ribosyltransferase from Streptomyces scabies
ComponentsScabin
KeywordsTRANSFERASE / mono-ADP-ribosyltransferase / apo-enzyme / NAD-binding protein
Function / homology: / : / Scabin-like / nucleotide binding / Putative secreted protein
Function and homology information
Biological speciesStreptomyces scabiei 87.22 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsDutta, D. / Lanoue, J. / Merrill, A.R.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)MOP-106661 Canada
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
DepositionAug 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
Revision 1.4Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 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 1.6Oct 9, 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: Scabin


Theoretical massNumber of molelcules
Total (without water)21,8571
Polymers21,8571
Non-polymers00
Water3,189177
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.787, 61.075, 37.812
Angle α, β, γ (deg.)90.000, 99.640, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-385-

HOH

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Components

#1: Protein Scabin / mono-ADP-ribosyltransferase


Mass: 21857.170 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces scabiei 87.22 (bacteria) / Strain: 87.22 / Cell line: K12 / Gene: SCAB_27771 / Plasmid: pET28 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: C9Z6T8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / 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: 46.2 % / Description: large multi-faceted crystals, 300 um x 300 um
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 100 mM MES, pH 6.5, 15% PEG400 / PH range: 6.0 - 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: Apr 21, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.45→43.273 Å / Num. obs: 33118 / % possible obs: 94.4 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 26.76 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.042 / Rrim(I) all: 0.048 / Χ2: 0.979 / Net I/σ(I): 18.81 / Num. measured all: 141816
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.45-1.540.6250.7642.1518873562445580.87681
1.54-1.640.8630.434.0421962531050630.4995.3
1.64-1.770.9570.2346.9420565492847330.26796
1.77-1.940.9910.10613.3519045456144050.12196.6
1.94-2.170.9970.05722.4317328413440140.06597.1
2.17-2.510.9980.03930.8315311364535590.04497.6
2.51-3.070.9990.03239.7513038310530490.03698.2
3.07-4.320.9990.02747.510090241023820.0398.8
4.320.9980.02749.435604136913550.03199

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
XSCALEdata scaling
PDB_EXTRACT3.15data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2CB4

2cb4


Resolution: 1.45→43.27 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.961 / SU B: 2.627 / SU ML: 0.049 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.06 / ESU R Free: 0.066 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2021 1655 5 %RANDOM
Rwork0.1649 ---
obs0.1668 31437 94.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 92.13 Å2 / Biso mean: 27.961 Å2 / Biso min: 12.45 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å20 Å20.5 Å2
2--0.04 Å20 Å2
3----0.03 Å2
Refinement stepCycle: final / Resolution: 1.45→43.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1313 0 0 177 1490
Biso mean---36.81 -
Num. residues----166
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0330.0191362
X-RAY DIFFRACTIONr_bond_other_d0.0030.021210
X-RAY DIFFRACTIONr_angle_refined_deg2.811.9391869
X-RAY DIFFRACTIONr_angle_other_deg1.36632800
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3175169
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.38423.63666
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.35915194
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.897159
X-RAY DIFFRACTIONr_chiral_restr0.1660.2195
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.0211562
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02313
X-RAY DIFFRACTIONr_mcbond_it2.3461.904667
X-RAY DIFFRACTIONr_mcbond_other2.3351.904666
X-RAY DIFFRACTIONr_mcangle_it3.5382.851833
LS refinement shellResolution: 1.45→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 92 -
Rwork0.349 1743 -
all-1835 -
obs--71.71 %
Refinement TLS params.Method: refined / Origin x: 27.9723 Å / Origin y: 33.3968 Å / Origin z: 14.1485 Å
111213212223313233
T0.0048 Å20.0073 Å20.0061 Å2-0.0583 Å20.0104 Å2--0.0078 Å2
L1.5839 °2-0.5704 °2-0.4941 °2-0.8264 °2-0.1107 °2--0.7187 °2
S0.0431 Å °0.211 Å °0.0634 Å °0.0105 Å °-0.0173 Å °0.0095 Å °-0.0183 Å °-0.1955 Å °-0.0258 Å °

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