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- PDB-7pwx: dUTPase from M. tuberculosis in complex with Stl -

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Basic information

Entry
Database: PDB / ID: 7pwx
TitledUTPase from M. tuberculosis in complex with Stl
Components
  • Deoxyuridine 5'-triphosphate nucleotidohydrolase
  • Orf20
KeywordsSTRUCTURAL PROTEIN / dUTPase / dUTP / DNA / Mycobacterium tuberculosis
Function / homology
Function and homology information


dUTP metabolic process / dUTP catabolic process / dUMP biosynthetic process / dUTP diphosphatase / dUTP diphosphatase activity / magnesium ion binding / DNA binding
Similarity search - Function
Deoxyuridine triphosphate nucleotidohydrolase / dUTPase-like / dUTPase / dUTPase, trimeric / Helix-turn-helix / dUTPase-like superfamily / 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
DI(HYDROXYETHYL)ETHER / Deoxyuridine 5'-triphosphate nucleotidohydrolase / Orf20
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
Staphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.75 Å
AuthorsMarina, A. / Sanz-Frasquet, C.
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 7, 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: pdbx_initial_refinement_model / struct / Item: _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 1.4Jun 19, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / citation / Item: _citation.country

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
HHH: Deoxyuridine 5'-triphosphate nucleotidohydrolase
III: Deoxyuridine 5'-triphosphate nucleotidohydrolase
JJJ: Deoxyuridine 5'-triphosphate nucleotidohydrolase
KKK: Deoxyuridine 5'-triphosphate nucleotidohydrolase
LLL: Deoxyuridine 5'-triphosphate nucleotidohydrolase
MMM: Deoxyuridine 5'-triphosphate nucleotidohydrolase
CCC: Orf20
DDD: Orf20
EEE: Orf20
FFF: Orf20
GGG: Orf20
AAA: Orf20
hetero molecules


Theoretical massNumber of molelcules
Total (without water)189,74128
Polymers188,33212
Non-polymers1,41016
Water1,71195
1
HHH: Deoxyuridine 5'-triphosphate nucleotidohydrolase
III: Deoxyuridine 5'-triphosphate nucleotidohydrolase
JJJ: Deoxyuridine 5'-triphosphate nucleotidohydrolase
EEE: Orf20
FFF: Orf20
GGG: Orf20
hetero molecules


  • defined by author
  • 95 kDa, 6 polymers
Theoretical massNumber of molelcules
Total (without water)94,99516
Polymers94,1666
Non-polymers82910
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
KKK: Deoxyuridine 5'-triphosphate nucleotidohydrolase
LLL: Deoxyuridine 5'-triphosphate nucleotidohydrolase
MMM: Deoxyuridine 5'-triphosphate nucleotidohydrolase
CCC: Orf20
DDD: Orf20
AAA: Orf20
hetero molecules


  • defined by author
  • 94.7 kDa, 6 polymers
Theoretical massNumber of molelcules
Total (without water)94,74712
Polymers94,1666
Non-polymers5816
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.407, 150.429, 107.370
Angle α, β, γ (deg.)90.000, 98.850, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 12 molecules HHHIIIJJJKKKLLLMMMCCCDDDEEEFFFGGGAAA

#1: Protein
Deoxyuridine 5'-triphosphate nucleotidohydrolase / dUTPase / dUTP pyrophosphatase


Mass: 14209.321 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: dut, Rv2697c, MTCY05A6.18c / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P9WNS5, dUTP diphosphatase
#2: Protein
Orf20


Mass: 17179.326 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9F0J8

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Non-polymers , 4 types, 111 molecules

#3: Chemical
ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / 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: 3.51 Å3/Da / Density % sol: 64.98 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 10.000 and 0.1 M Na-Hepes pH7.5

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.75→75.33 Å / Num. obs: 61491 / % possible obs: 95.07 % / Redundancy: 4.4 % / CC1/2: 0.976 / Net I/σ(I): 8.3
Reflection shellResolution: 2.75→2.821 Å / Num. unique obs: 4301 / CC1/2: 0.586

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.75→75.328 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.91 / Cross valid method: FREE R-VALUE / ESU R: 0.662 / ESU R Free: 0.338
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.25875 3102 5.045 %
Rwork0.20069 58384 -
all0.204 --
obs0.20371 61491 95.069 %
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: 56.503 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å20 Å2-3.356 Å2
2--1.149 Å20 Å2
3----0.385 Å2
Refinement stepCycle: LAST / Resolution: 2.75→75.328 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12091 0 92 108 12291
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01312398
X-RAY DIFFRACTIONr_bond_other_d0.0360.01711528
X-RAY DIFFRACTIONr_angle_refined_deg1.461.64316828
X-RAY DIFFRACTIONr_angle_other_deg2.4181.57726409
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.98251608
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.00322.08548
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.26151870
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.241577
X-RAY DIFFRACTIONr_chiral_restr0.0570.21665
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214101
X-RAY DIFFRACTIONr_gen_planes_other0.0080.022683
X-RAY DIFFRACTIONr_nbd_refined0.2050.22473
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2230.210687
X-RAY DIFFRACTIONr_nbtor_refined0.1640.25934
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0740.25768
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.2309
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0660.219
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1330.210
X-RAY DIFFRACTIONr_nbd_other0.1970.241
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0560.21
X-RAY DIFFRACTIONr_mcbond_it4.1396.2886495
X-RAY DIFFRACTIONr_mcbond_other4.1396.2876490
X-RAY DIFFRACTIONr_mcangle_it6.429.4158078
X-RAY DIFFRACTIONr_mcangle_other6.429.4168079
X-RAY DIFFRACTIONr_scbond_it3.9596.3655903
X-RAY DIFFRACTIONr_scbond_other3.9596.3655904
X-RAY DIFFRACTIONr_scangle_it6.1819.4578749
X-RAY DIFFRACTIONr_scangle_other6.189.4588750
X-RAY DIFFRACTIONr_lrange_it8.9873.74213116
X-RAY DIFFRACTIONr_lrange_other8.9873.74313117
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-2.8210.3712600.3354301X-RAY DIFFRACTION95.8999
2.821-2.8990.3762230.3044251X-RAY DIFFRACTION96.4848
2.899-2.9830.3221960.2754171X-RAY DIFFRACTION96.2955
2.983-3.0740.3332010.2333980X-RAY DIFFRACTION95.1308
3.074-3.1750.3341970.2293798X-RAY DIFFRACTION93.8895
3.175-3.2860.321790.2223566X-RAY DIFFRACTION91.7218
3.286-3.410.2851860.2123668X-RAY DIFFRACTION96.6157
3.41-3.5490.3141970.2193456X-RAY DIFFRACTION95.7787
3.549-3.7070.2641720.2033383X-RAY DIFFRACTION96.4984
3.707-3.8880.2471490.1813221X-RAY DIFFRACTION96.3959
3.888-4.0980.2171820.1693011X-RAY DIFFRACTION95.3419
4.098-4.3460.2081520.1572707X-RAY DIFFRACTION90.7619
4.346-4.6450.2061600.1442764X-RAY DIFFRACTION97.3693
4.645-5.0170.2121450.1422502X-RAY DIFFRACTION96.2896
5.017-5.4940.2321110.1642345X-RAY DIFFRACTION96.4272
5.494-6.1410.2581020.2052060X-RAY DIFFRACTION92.4327
6.141-7.0870.304980.2291800X-RAY DIFFRACTION93.0392
7.087-8.670.238890.2041565X-RAY DIFFRACTION95.6622

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