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- PDB-8xhm: Crystal structure of Nocardia seriolae dUTP diphosphatase -

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Basic information

Entry
Database: PDB / ID: 8xhm
TitleCrystal structure of Nocardia seriolae dUTP diphosphatase
ComponentsDeoxyuridine 5'-triphosphate nucleotidohydrolase
KeywordsHYDROLASE / Nocardia seriolae / dUTP diphosphatase / dUMP
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
DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / Deoxyuridine 5'-triphosphate nucleotidohydrolase
Similarity search - Component
Biological speciesNocardia seriolae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 Å
AuthorsWeng, J. / Wei, Z.
Funding support China, 1items
OrganizationGrant numberCountry
Other governmentSKLBEE2022007 China
CitationJournal: J Enzyme Inhib Med Chem / Year: 2024
Title: Structure-guided discovery of novel dUTPase inhibitors with anti- Nocardia activity by computational design.
Authors: Wang, Z.Z. / Weng, J. / Qi, J. / Fu, X.X. / Xing, B.B. / Hu, Y. / Huang, C.H. / Chen, C.Y. / Wei, Z.
History
DepositionDec 18, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 13, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)20,5597
Polymers19,6991
Non-polymers8606
Water81145
1
A: Deoxyuridine 5'-triphosphate nucleotidohydrolase
hetero molecules

A: Deoxyuridine 5'-triphosphate nucleotidohydrolase
hetero molecules

A: Deoxyuridine 5'-triphosphate nucleotidohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,67721
Polymers59,0983
Non-polymers2,57918
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area18770 Å2
ΔGint-37 kcal/mol
Surface area15090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.807, 120.807, 120.807
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number213
Space group name H-MP4132
Components on special symmetry positions
IDModelComponents
11A-302-

PO4

21A-302-

PO4

31A-306-

TRS

41A-306-

TRS

51A-443-

HOH

61A-445-

HOH

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 19699.186 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nocardia seriolae (bacteria)
Gene: dut, D6158_15615, NS07_v2contig00045-0031, NS506_05871
Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A0B8NBT7, dUTP diphosphatase

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Non-polymers , 5 types, 51 molecules

#2: Chemical ChemComp-UMP / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / DUMP


Mass: 308.182 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H13N2O8P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.73 Å3/Da / Density % sol: 67.5 % / Description: clear cubic crystal
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Diffractable crystals grew in 25% (w/v) polyethylene glycol 3350, 0.1 M Tris-HCl pH 8.5 at 293 K.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 07A / Wavelength: 0.976 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Apr 14, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.12→29.3 Å / Num. obs: 17649 / % possible obs: 99.8 % / Redundancy: 50.7 % / Biso Wilson estimate: 52.7 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.011 / Rrim(I) all: 0.076 / Net I/σ(I): 36.67
Reflection shellResolution: 2.12→2.196 Å / Mean I/σ(I) obs: 3.35 / Num. unique obs: 1723 / CC1/2: 0.936 / % possible all: 98.8

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SIX

1six


Resolution: 2.12→29.3 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2053 882 5 %
Rwork0.1859 --
obs0.1868 17649 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.12→29.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1027 0 55 45 1127
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071094
X-RAY DIFFRACTIONf_angle_d0.9091489
X-RAY DIFFRACTIONf_dihedral_angle_d6.404166
X-RAY DIFFRACTIONf_chiral_restr0.064177
X-RAY DIFFRACTIONf_plane_restr0.009190
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.12-2.250.26211420.2292703X-RAY DIFFRACTION99
2.25-2.430.21841440.21252733X-RAY DIFFRACTION100
2.43-2.670.27771450.23322752X-RAY DIFFRACTION100
2.67-3.060.24781460.22882773X-RAY DIFFRACTION100
3.06-3.850.20691480.19952817X-RAY DIFFRACTION100
3.85-29.30.17671570.15572989X-RAY DIFFRACTION100

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