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- PDB-8k6w: dUTPase of helicobacter pylori 26695 -

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Basic information

Entry
Database: PDB / ID: 8k6w
TitledUTPase of helicobacter pylori 26695
ComponentsDeoxyuridine 5'-triphosphate nucleotidohydrolase
KeywordsHYDROLASE / enzyme
Function / homology
Function and homology information


dUTP catabolic process / dUMP biosynthetic process / dUTP diphosphatase / dUTP diphosphatase activity / magnesium ion binding
Similarity search - Function
Deoxyuridine triphosphate nucleotidohydrolase / dUTPase-like / dUTPase / dUTPase, trimeric / dUTPase-like superfamily
Similarity search - Domain/homology
Deoxyuridine 5'-triphosphate nucleotidohydrolase
Similarity search - Component
Biological speciesHelicobacter pylori 26695 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsKumari, K. / Gourinath, S.
Funding support India, 1items
OrganizationGrant numberCountry
Other government India
CitationJournal: Int.J.Biol.Macromol. / Year: 2024
Title: Structural analysis of dUTPase from Helicobacter pylori reveals unusual activity for dATP.
Authors: Kumari, K. / Aggarwal, S. / Khan, F.M. / Munde, M. / Gourinath, S.
History
DepositionJul 25, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 31, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 26, 2025Group: Database references / Structure summary
Category: audit_author / citation ...audit_author / citation / citation_author / pdbx_entry_details
Item: _audit_author.name / _citation.country ..._audit_author.name / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Deoxyuridine 5'-triphosphate nucleotidohydrolase
B: Deoxyuridine 5'-triphosphate nucleotidohydrolase
C: Deoxyuridine 5'-triphosphate nucleotidohydrolase


Theoretical massNumber of molelcules
Total (without water)50,1663
Polymers50,1663
Non-polymers00
Water41423
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9140 Å2
ΔGint-44 kcal/mol
Surface area15890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.360, 102.360, 78.370
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63

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Components

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


Mass: 16722.076 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori 26695 (bacteria) / Strain: ATCC 700392 / 26695 / Gene: dut, HP_0865 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O25536, dUTP diphosphatase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.36 Å3/Da / Density % sol: 47.89 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: MORPHEUS H4 condition:0.1 M Amino acid mix, 0.1 M buffer system pH 6.5, 50% V/V precipitant mix 4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.5→58.7 Å / Num. obs: 16291 / % possible obs: 100 % / Redundancy: 46.3 % / CC1/2: 0.99 / Net I/σ(I): 18.7
Reflection shellResolution: 2.5→2.6 Å / Num. unique obs: 1837 / CC1/2: 0.833

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MBQ

3mbq


Resolution: 2.5→58.7 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.918 / SU B: 21.121 / SU ML: 0.214 / Cross valid method: FREE R-VALUE / ESU R: 0.436 / ESU R Free: 0.271
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2384 1092 6.711 %
Rwork0.175 15181 -
all0.179 --
obs-16273 99.969 %
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: 47.122 Å2
Baniso -1Baniso -2Baniso -3
1--0.165 Å2-0.082 Å2-0 Å2
2---0.165 Å20 Å2
3---0.535 Å2
Refinement stepCycle: LAST / Resolution: 2.5→58.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2981 0 0 23 3004
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0123023
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162961
X-RAY DIFFRACTIONr_angle_refined_deg1.3391.6454084
X-RAY DIFFRACTIONr_angle_other_deg0.4471.5746818
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1845385
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.519512
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.38410543
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.10910130
X-RAY DIFFRACTIONr_chiral_restr0.0580.2481
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023473
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02623
X-RAY DIFFRACTIONr_nbd_refined0.2030.2434
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1950.22646
X-RAY DIFFRACTIONr_nbtor_refined0.170.21415
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0870.21758
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1240.263
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3890.24
X-RAY DIFFRACTIONr_nbd_other0.2450.214
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3460.23
X-RAY DIFFRACTIONr_mcbond_it2.532.9911549
X-RAY DIFFRACTIONr_mcbond_other2.5132.9911549
X-RAY DIFFRACTIONr_mcangle_it3.9545.3511931
X-RAY DIFFRACTIONr_mcangle_other3.9545.3551932
X-RAY DIFFRACTIONr_scbond_it3.6053.4711474
X-RAY DIFFRACTIONr_scbond_other3.5893.4691473
X-RAY DIFFRACTIONr_scangle_it5.8126.1672153
X-RAY DIFFRACTIONr_scangle_other5.816.1692154
X-RAY DIFFRACTIONr_lrange_it7.49727.7062967
X-RAY DIFFRACTIONr_lrange_other7.527.7182967
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.5650.326750.2831127X-RAY DIFFRACTION99.751
2.565-2.6350.294680.2561103X-RAY DIFFRACTION99.9147
2.635-2.7110.263810.2211032X-RAY DIFFRACTION100
2.711-2.7950.3321000.2371017X-RAY DIFFRACTION100
2.795-2.8860.298770.223975X-RAY DIFFRACTION100
2.886-2.9870.299770.216945X-RAY DIFFRACTION100
2.987-3.10.309810.199924X-RAY DIFFRACTION100
3.1-3.2260.235570.202915X-RAY DIFFRACTION100
3.226-3.3690.259530.195847X-RAY DIFFRACTION100
3.369-3.5330.253510.186844X-RAY DIFFRACTION100
3.533-3.7230.238650.163768X-RAY DIFFRACTION100
3.723-3.9480.242770.157722X-RAY DIFFRACTION100
3.948-4.2190.223370.144713X-RAY DIFFRACTION100
4.219-4.5550.172520.114646X-RAY DIFFRACTION100
4.555-4.9870.144260.111615X-RAY DIFFRACTION100
4.987-5.570.169290.132556X-RAY DIFFRACTION100
5.57-6.4230.163350.161492X-RAY DIFFRACTION100
6.423-7.8430.184300.158411X-RAY DIFFRACTION100
7.843-10.9940.224120.173331X-RAY DIFFRACTION100
10.994-58.70.38590.256198X-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)
10.83830.42650.51111.09780.4720.54180.26190.1110.03250.1982-0.33380.059-0.00230.04250.07190.268-0.0565-0.0330.22-0.00340.0173-23.116124.8669.8179
20.58620.49730.5841.96440.2490.62770.10250.10590.0825-0.1585-0.18640.21310.11120.13810.08390.1640.0911-0.09160.151-0.05040.092-29.975218.0126-6.9552
30.95880.8647-0.22761.78590.35540.3813-0.17590.1520.036-0.25850.12090.1244-0.02680.00640.05510.18450.0127-0.03670.23830.04950.0254-18.016332.8084-7.7041
Refinement TLS groupSelection: ALL

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