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- PDB-8y1q: Crystal structure of Aquifex aeolicus dUTPase complexed with dUMP. -

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Basic information

Entry
Database: PDB / ID: 8y1q
TitleCrystal structure of Aquifex aeolicus dUTPase complexed with dUMP.
ComponentsDeoxyuridine 5'-triphosphate nucleotidohydrolase
KeywordsHYDROLASE / dUTPase / dUTP / dUMP / hyperthermophile / Aquifex aeolicus
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
2'-DEOXYURIDINE-5'-MONOPHOSPHATE / Deoxyuridine 5'-triphosphate nucleotidohydrolase
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.42 Å
AuthorsFukui, K. / Murakawa, T. / Yano, T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Protein Sci. / Year: 2024
Title: dUTP pyrophosphatases from hyperthermophilic eubacterium and archaeon: Structural and functional examinations on the suitability for PCR application.
Authors: Fukui, K. / Kondo, N. / Murakawa, T. / Baba, S. / Kumasaka, T. / Yano, T.
History
DepositionJan 25, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 6, 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
B: Deoxyuridine 5'-triphosphate nucleotidohydrolase
C: Deoxyuridine 5'-triphosphate nucleotidohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,1828
Polymers49,2093
Non-polymers9735
Water1629
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11840 Å2
ΔGint-69 kcal/mol
Surface area16460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.260, 61.260, 112.660
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41
Space group name HallP4w
Symmetry operation#1: x,y,z
#2: -y,x,z+1/4
#3: y,-x,z+3/4
#4: -x,-y,z+1/2

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Components

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


Mass: 16402.982 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Gene: dut, aq_220 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) pLysS / References: UniProt: O66592, dUTP diphosphatase
#2: Chemical ChemComp-DU / 2'-DEOXYURIDINE-5'-MONOPHOSPHATE


Type: DNA linking / Mass: 308.182 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C9H13N2O8P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 2.09 Å3/Da / Density % sol: 41.1 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 200 mM magnesium chloride, 100 mM Tris-HCl (pH 8.5), and 25% (w/v) polyethylene glycol 3,350.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 15, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.42→43.32 Å / Num. obs: 15876 / % possible obs: 99.9 % / Redundancy: 15 % / Biso Wilson estimate: 78.81 Å2 / CC1/2: 0.998 / Net I/σ(I): 18.1
Reflection shellResolution: 2.42→2.51 Å / Redundancy: 10.5 % / Num. unique obs: 1570 / CC1/2: 0.758 / % possible all: 99.9

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Processing

Software
NameVersionClassification
XDSdata reduction
PHENIX1.21-5207refinement
Coot0.9.8.92model building
PHENIX1.21-5207phasing
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.42→43.32 Å / SU ML: 0.496 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 38.2555
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2731 1572 9.91 %
Rwork0.2331 14286 -
obs0.2371 15858 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 96.12 Å2
Refinement stepCycle: LAST / Resolution: 2.42→43.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3064 0 62 9 3135
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023180
X-RAY DIFFRACTIONf_angle_d0.50334360
X-RAY DIFFRACTIONf_chiral_restr0.0483533
X-RAY DIFFRACTIONf_plane_restr0.0058561
X-RAY DIFFRACTIONf_dihedral_angle_d14.7211167
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.42-2.50.4721400.40961294X-RAY DIFFRACTION100
2.5-2.590.45181390.38571300X-RAY DIFFRACTION99.79
2.59-2.690.35771410.33591309X-RAY DIFFRACTION100
2.69-2.810.35351460.33681280X-RAY DIFFRACTION99.93
2.81-2.960.37451420.3431288X-RAY DIFFRACTION99.58
2.96-3.150.40441430.33711284X-RAY DIFFRACTION99.93
3.15-3.390.38071520.30521298X-RAY DIFFRACTION99.79
3.39-3.730.30311470.28681287X-RAY DIFFRACTION99.86
3.73-4.270.24351370.22151308X-RAY DIFFRACTION99.93
4.27-5.380.22581450.17631317X-RAY DIFFRACTION100
5.38-43.320.22161400.18421321X-RAY DIFFRACTION99.86
Refinement TLS params.Method: refined / Origin x: 2.02038653401 Å / Origin y: 30.4396863486 Å / Origin z: -0.536320535887 Å
111213212223313233
T0.446715815842 Å20.0864224640796 Å20.00485151828578 Å2-0.500386130027 Å20.0159800843402 Å2--0.475705725247 Å2
L2.33340246645 °20.376366896226 °2-1.43597131996 °2-3.97454999858 °2-0.0148530197394 °2--5.48302102543 °2
S0.0262588017161 Å °0.0311002231724 Å °0.160889670285 Å °0.0768665375442 Å °-0.31501193379 Å °-0.150721573894 Å °-0.34570989178 Å °-0.444787267788 Å °0.285454035028 Å °
Refinement TLS groupSelection details: all

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