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- PDB-8y1w: Crystal structure of Thermococcus pacificus dUTPase complexed wit... -

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Basic information

Entry
Database: PDB / ID: 8y1w
TitleCrystal structure of Thermococcus pacificus dUTPase complexed with dUMP.
ComponentsdCTP deaminase
KeywordsHYDROLASE / dUTPase / dUTP / dUMP / hyperthermophile / Thermococcus pacificus
Function / homology
Function and homology information


dCTP deaminase / dUTP biosynthetic process / dCTP deaminase activity / dUMP biosynthetic process / nucleotide binding
Similarity search - Function
dCTP deaminase / dCTP deaminase-like / dUTPase, trimeric / dUTPase-like superfamily
Similarity search - Domain/homology
PHOSPHATE ION / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / dCTP deaminase
Similarity search - Component
Biological speciesThermococcus pacificus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.36 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

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Assembly

Deposited unit
A: dCTP deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3075
Polymers17,7171
Non-polymers5904
Water1,802100
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.616, 52.616, 87.519
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Space group name HallP6c
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/2
#3: y,-x+y,z+1/2
#4: -y,x-y,z
#5: -x+y,-x,z
#6: -x,-y,z+1/2
Components on special symmetry positions
IDModelComponents
11A-311-

HOH

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Components

#1: Protein dCTP deaminase / Deoxycytidine triphosphate deaminase


Mass: 17716.566 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus pacificus (archaea) / Gene: dut, dcd, A3L08_04840 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) pLysS / References: UniProt: K7PBY4, dCTP deaminase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-UMP / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / DUMP


Mass: 308.182 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C9H13N2O8P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 1.92 Å3/Da / Density % sol: 35.9 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.2
Details: 56 mM sodium phosphate, 1.34 M potassium phosphate (pH 8.2)

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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: Oct 19, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.36→43.76 Å / Num. obs: 29438 / % possible obs: 99.24 % / Redundancy: 11.1 % / Biso Wilson estimate: 18.06 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.1 / Rrim(I) all: 0.1 / Net I/σ(I): 20.5
Reflection shellResolution: 1.36→1.4 Å / Rmerge(I) obs: 0.79 / Mean I/σ(I) obs: 3.8 / Num. unique obs: 2280 / CC1/2: 0.95 / Rrim(I) all: 0.81

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
PHENIX1.21-5207phasing
Coot0.9.8.92model building
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.36→43.76 Å / SU ML: 0.1558 / Cross valid method: FREE R-VALUE / σ(F): 1.44 / Phase error: 17.9944
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1794 1710 5.81 %
Rwork0.1498 27727 -
obs0.1515 29437 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.45 Å2
Refinement stepCycle: LAST / Resolution: 1.36→43.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1164 0 36 100 1300
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01491236
X-RAY DIFFRACTIONf_angle_d1.36721676
X-RAY DIFFRACTIONf_chiral_restr0.1125182
X-RAY DIFFRACTIONf_plane_restr0.0099211
X-RAY DIFFRACTIONf_dihedral_angle_d14.7971474
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.36-1.40.22111380.17532280X-RAY DIFFRACTION98.94
1.4-1.450.20011440.1452286X-RAY DIFFRACTION99.79
1.45-1.50.16231470.13082317X-RAY DIFFRACTION99.88
1.5-1.560.17011400.1382298X-RAY DIFFRACTION99.96
1.56-1.630.25141390.16642326X-RAY DIFFRACTION99.92
1.63-1.710.23371420.15092293X-RAY DIFFRACTION100
1.71-1.820.1871440.13262321X-RAY DIFFRACTION100
1.82-1.960.13811450.14322309X-RAY DIFFRACTION100
1.96-2.160.17691390.14322287X-RAY DIFFRACTION100
2.16-2.470.19621500.15452325X-RAY DIFFRACTION100
2.47-3.110.17561400.17262336X-RAY DIFFRACTION100
3.11-43.760.16741420.14122349X-RAY DIFFRACTION99.92

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