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- PDB-7pwj: dUTPase from human in complex with Stl -

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Basic information

Entry
Database: PDB / ID: 7pwj
TitledUTPase from human in complex with Stl
Components
  • Deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrial
  • Orf20
KeywordsSTRUCTURAL PROTEIN / dUTPase / dUTP / human / DNA
Function / homology
Function and homology information


pyrimidine deoxyribonucleotide binding / dUTP catabolic process / dUMP biosynthetic process / dUTP diphosphatase / dUTP diphosphatase activity / Interconversion of nucleotide di- and triphosphates / peroxisome proliferator activated receptor binding / nucleobase-containing compound metabolic process / signaling receptor inhibitor activity / dTMP biosynthetic process ...pyrimidine deoxyribonucleotide binding / dUTP catabolic process / dUMP biosynthetic process / dUTP diphosphatase / dUTP diphosphatase activity / Interconversion of nucleotide di- and triphosphates / peroxisome proliferator activated receptor binding / nucleobase-containing compound metabolic process / signaling receptor inhibitor activity / dTMP biosynthetic process / regulation of protein-containing complex assembly / liver development / DNA replication / magnesium ion binding / mitochondrion / DNA binding / RNA binding / extracellular exosome / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
Deoxyuridine triphosphate nucleotidohydrolase / dUTPase-like / dUTPase / dUTPase, trimeric / dUTPase-like superfamily / Helix-turn-helix / Helix-turn-helix XRE-family like proteins / Cro/C1-type HTH domain profile. / Cro/C1-type helix-turn-helix domain / Lambda repressor-like, DNA-binding domain superfamily
Similarity search - Domain/homology
Deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrial / Orf20
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.944 Å
AuthorsSanz-Frasquet, C. / Marina, A.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and Universities Spain
CitationJournal: Microbiol Spectr / Year: 2023
Title: The Bacteriophage-Phage-Inducible Chromosomal Island Arms Race Designs an Interkingdom Inhibitor of dUTPases.
Authors: Sanz-Frasquet, C. / Ciges-Tomas, J.R. / Alite, C. / Penades, J.R. / Marina, A.
History
DepositionOct 6, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 28, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2023Group: Refinement description / Structure summary / Category: refine / struct / Item: _refine.pdbx_starting_model / _struct.title
Revision 1.2Jan 18, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Feb 22, 2023Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.4Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
CCC: Orf20
AAA: Deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrial
BBB: Deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrial
DDD: Deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrial
EEE: Orf20
FFF: Orf20
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,40438
Polymers102,0346
Non-polymers2,37032
Water5,675315
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25260 Å2
ΔGint-131 kcal/mol
Surface area33430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.720, 81.797, 198.398
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 6 molecules CCCEEEFFFAAABBBDDD

#1: Protein Orf20


Mass: 18100.340 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Plasmid: pETNKI-1.10 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9F0J8
#2: Protein Deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrial / dUTPase / dUTP pyrophosphatase


Mass: 15910.923 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DUT / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P33316, dUTP diphosphatase

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Non-polymers , 4 types, 347 molecules

#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 315 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 3.33 Å3/Da / Density % sol: 63.02 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / Details: 1.6M ammonium sulphate and 1M lithium sulphate.

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.99186 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Nov 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99186 Å / Relative weight: 1
ReflectionResolution: 1.944→99.2 Å / Num. obs: 92354 / % possible obs: 98.48 % / Redundancy: 12.9 % / CC1/2: 0.999 / Net I/σ(I): 18.9
Reflection shellResolution: 1.944→1.995 Å / Num. unique obs: 5386 / CC1/2: 0.897

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6H49, 1Q5U

6h49

1q5u


Resolution: 1.944→99.199 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.945 / SU B: 7.503 / SU ML: 0.185 / Cross valid method: FREE R-VALUE / ESU R: 0.147 / ESU R Free: 0.148
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.26191 4665 5.1 %
Rwork0.21424 87692 -
all0.217 --
obs0.21659 92311 98.495 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 48.965 Å2
Baniso -1Baniso -2Baniso -3
1-4.944 Å2-0 Å20 Å2
2---1.866 Å2-0 Å2
3----3.078 Å2
Refinement stepCycle: LAST / Resolution: 1.944→99.199 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6555 0 146 315 7016
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0136847
X-RAY DIFFRACTIONr_bond_other_d0.0020.0176276
X-RAY DIFFRACTIONr_angle_refined_deg1.4851.6539210
X-RAY DIFFRACTIONr_angle_other_deg1.3381.5814403
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7185852
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.02222.029340
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.444151086
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6531540
X-RAY DIFFRACTIONr_chiral_restr0.0680.2878
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.027732
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021587
X-RAY DIFFRACTIONr_nbd_refined0.1980.21359
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1950.25923
X-RAY DIFFRACTIONr_nbtor_refined0.1710.23338
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0840.23011
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.2328
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0780.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1490.219
X-RAY DIFFRACTIONr_nbd_other0.210.259
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2380.27
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0340.21
X-RAY DIFFRACTIONr_mcbond_it3.9215.2593414
X-RAY DIFFRACTIONr_mcbond_other3.9215.2583413
X-RAY DIFFRACTIONr_mcangle_it5.6417.8654261
X-RAY DIFFRACTIONr_mcangle_other5.6417.8674262
X-RAY DIFFRACTIONr_scbond_it3.9325.4683433
X-RAY DIFFRACTIONr_scbond_other3.9325.4693434
X-RAY DIFFRACTIONr_scangle_it5.5898.0474948
X-RAY DIFFRACTIONr_scangle_other5.5898.0474949
X-RAY DIFFRACTIONr_lrange_it7.78560.7217597
X-RAY DIFFRACTIONr_lrange_other7.78660.7227598
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.944-1.9950.5033130.4855386X-RAY DIFFRACTION83.1849
3.285-3.5480.2631880.2033864X-RAY DIFFRACTION100
3.548-3.8860.2641920.1753545X-RAY DIFFRACTION100
3.886-4.3440.2011530.1593231X-RAY DIFFRACTION100
4.344-5.0150.2081450.1462852X-RAY DIFFRACTION100
5.015-6.1380.2361420.1792428X-RAY DIFFRACTION100
6.138-8.6640.1971040.1981936X-RAY DIFFRACTION99.951
8.664-99.1990.212550.2271145X-RAY DIFFRACTION99.9167

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