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- PDB-24ok: Crystal structure of human dUTPase complexed with Zinc. -

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Basic information

Entry
Database: PDB / ID: 24ok
TitleCrystal structure of human dUTPase complexed with Zinc.
ComponentsDeoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrial
KeywordsHYDROLASE / DUT / dUTPase / human dUTPase / Deoxyuridine 5'-triphosphate nucleotidohydrolase
Function / homology
Function and homology information


pyrimidine deoxyribonucleotide binding / dUTP catabolic process / dUMP biosynthetic process / dUTP diphosphatase / dUTP diphosphatase activity / signaling receptor inhibitor activity / Interconversion of nucleotide di- and triphosphates / peroxisome proliferator activated receptor binding / nucleobase-containing compound metabolic process / dTMP biosynthetic process ...pyrimidine deoxyribonucleotide binding / dUTP catabolic process / dUMP biosynthetic process / dUTP diphosphatase / dUTP diphosphatase activity / signaling receptor inhibitor activity / Interconversion of nucleotide di- and triphosphates / peroxisome proliferator activated receptor binding / nucleobase-containing compound metabolic process / dTMP biosynthetic process / regulation of protein-containing complex assembly / liver development / DNA replication / magnesium ion binding / mitochondrion / RNA binding / extracellular exosome / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
Deoxyuridine triphosphate nucleotidohydrolase / dUTPase-like / dUTPase / dUTPase, trimeric / dUTPase-like superfamily
Similarity search - Domain/homology
Deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsKrinkel, B.A. / Yosaatmadja, Y. / Loomes, K.M. / Squire, C.J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Human dUTPase crystal structure and...
Authors: Krinkel, B.A. / Yosaatmadja, Y. / Loomes, K.M. / Squire, C.J.
History
DepositionMar 13, 2026Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 1, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0159
Polymers19,5021
Non-polymers5138
Water1,20767
1
A: Deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrial
hetero molecules

A: Deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrial
hetero molecules

A: Deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,04627
Polymers58,5063
Non-polymers1,54024
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area11870 Å2
ΔGint-457 kcal/mol
Surface area14090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.253, 84.253, 84.253
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-202-

ZN

21A-203-

ZN

31A-204-

ZN

41A-205-

ZN

51A-351-

HOH

61A-359-

HOH

71A-361-

HOH

81A-365-

HOH

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Components

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


Mass: 19502.012 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DUT / Production host: Escherichia coli (E. coli) / References: UniProt: P33316, dUTP diphosphatase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.56 Å3/Da / Density % sol: 51.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Crystal condition: 0.09M 1,6-Hexanediol, 1-Butanol, 1,2-Propanediol, 2-Propanol, 1,4-Butanediol, 1,3-Propanediol. 0.1M Tris (base), BICINE. 30% v/v Glycerol, PEG 4000. (Morpheus D3) Seeded ...Details: Crystal condition: 0.09M 1,6-Hexanediol, 1-Butanol, 1,2-Propanediol, 2-Propanol, 1,4-Butanediol, 1,3-Propanediol. 0.1M Tris (base), BICINE. 30% v/v Glycerol, PEG 4000. (Morpheus D3) Seeded with: 0.2M Zinc Acetate, 0.1M Sodium cacodylate, 10% v/v 2-Propanol, pH 6.5 (JCSG E7)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 15, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.01→48.691 Å / Num. obs: 13576 / % possible obs: 100 % / Redundancy: 19.4 % / CC1/2: 0.998 / Net I/σ(I): 19.5
Reflection shellResolution: 2.01→2.06 Å / Mean I/σ(I) obs: 1.1 / Num. unique obs: 988 / CC1/2: 0.431

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Processing

Software
NameVersionClassification
REFMAC5.8.0431refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.01→48.691 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.949 / SU B: 4.318 / SU ML: 0.113 / Cross valid method: THROUGHOUT / ESU R: 0.151 / ESU R Free: 0.137
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2335 662 4.885 %RANDOM
Rwork0.2122 12891 --
all0.213 ---
obs-13553 99.97 %-
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: 51.567 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.01→48.691 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms943 0 17 67 1027
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0121013
X-RAY DIFFRACTIONr_bond_other_d0.0050.016960
X-RAY DIFFRACTIONr_angle_refined_deg1.2971.8381356
X-RAY DIFFRACTIONr_angle_other_deg1.2481.7622203
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2225127
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.67459
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.17310160
X-RAY DIFFRACTIONr_dihedral_angle_6_deg11.6391045
X-RAY DIFFRACTIONr_chiral_restr0.0580.2146
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021196
X-RAY DIFFRACTIONr_gen_planes_other0.0190.02238
X-RAY DIFFRACTIONr_nbd_refined0.190.2131
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2140.2850
X-RAY DIFFRACTIONr_nbtor_refined0.1790.2489
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0880.2539
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.260
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0250.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.20.238
X-RAY DIFFRACTIONr_nbd_other0.3290.290
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1320.210
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0810.210
X-RAY DIFFRACTIONr_mcbond_it4.2475.293505
X-RAY DIFFRACTIONr_mcbond_other4.245.293505
X-RAY DIFFRACTIONr_mcangle_it6.0079.477633
X-RAY DIFFRACTIONr_mcangle_other6.0039.481634
X-RAY DIFFRACTIONr_scbond_it5.0445.819508
X-RAY DIFFRACTIONr_scbond_other5.0395.825509
X-RAY DIFFRACTIONr_scangle_it7.54710.42723
X-RAY DIFFRACTIONr_scangle_other7.54210.423724
X-RAY DIFFRACTIONr_lrange_it9.80955.1941063
X-RAY DIFFRACTIONr_lrange_other9.79855.2661056
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.01-2.0620.38340.3449510.3459870.9080.89899.79740.341
2.062-2.1190.351400.3159220.3179630.9170.92499.89620.306
2.119-2.180.29470.288930.2819400.9390.9461000.264
2.18-2.2470.279430.2858540.2858970.9530.9441000.261
2.247-2.320.259500.258390.258890.9570.9591000.223
2.32-2.4020.262600.2477920.2488520.9610.9611000.215
2.402-2.4920.264440.2227870.2248310.9580.9681000.191
2.492-2.5930.337270.2437670.2467940.9330.9621000.208
2.593-2.7080.25460.2427250.2427710.9570.9631000.21
2.708-2.840.255250.2267130.2277380.9630.9681000.197
2.84-2.9930.245350.2176600.2196950.9640.971000.199
2.993-3.1740.201360.2126240.2126600.9720.9711000.199
3.174-3.3920.207170.2036080.2036250.9710.9751000.198
3.392-3.6620.225160.2035700.2035860.9680.9761000.2
3.662-4.010.165410.194930.1885340.9810.9791000.195
4.01-4.4790.2280.1754670.1764950.9760.981000.188
4.479-5.1650.208230.1664080.1684310.9750.9841000.18
5.165-6.3080.187220.1933620.1923840.9830.9771000.211
6.308-8.8470.384190.2132750.2232940.9220.9721000.235
8.847-48.6910.24390.2431810.2431900.9520.9611000.257

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