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- PDB-9ln3: A thermostable enzyme dUTPase P45 -

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Basic information

Entry
Database: PDB / ID: 9ln3
TitleA thermostable enzyme dUTPase P45
ComponentsdCTP deaminase
KeywordsMETAL BINDING PROTEIN / A thermostable enzyme dUTPase P45
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
2'-DEOXYURIDINE 5'-MONOPHOSPHATE / dCTP deaminase
Similarity search - Component
Biological speciesPyrococcus furiosus DSM 3638 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsWang, Y.X. / Dong, B.J.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2024YFC3407300 China
CitationJournal: Int.J.Biol.Macromol. / Year: 2025
Title: Structural and functional characterization of thermostable dUTPase P45 from Pyrococcus furiosus with enhanced PCR efficiency.
Authors: Dong, B. / Li, J. / Zhang, L. / Zhang, B. / Xu, B. / Ye, S. / Wang, Y.
History
DepositionJan 20, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 19, 2025Provider: 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)18,2022
Polymers17,8941
Non-polymers3081
Water37821
1
A: dCTP deaminase
hetero molecules

A: dCTP deaminase
hetero molecules

A: dCTP deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,6066
Polymers53,6813
Non-polymers9253
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area9350 Å2
ΔGint-66 kcal/mol
Surface area15560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.040, 99.040, 99.040
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23
Space group name HallI223
Symmetry operation#1: x,y,z
#2: z,x,y
#3: y,z,x
#4: -y,-z,x
#5: z,-x,-y
#6: -y,z,-x
#7: -z,-x,y
#8: -z,x,-y
#9: y,-z,-x
#10: x,-y,-z
#11: -x,y,-z
#12: -x,-y,z
#13: x+1/2,y+1/2,z+1/2
#14: z+1/2,x+1/2,y+1/2
#15: y+1/2,z+1/2,x+1/2
#16: -y+1/2,-z+1/2,x+1/2
#17: z+1/2,-x+1/2,-y+1/2
#18: -y+1/2,z+1/2,-x+1/2
#19: -z+1/2,-x+1/2,y+1/2
#20: -z+1/2,x+1/2,-y+1/2
#21: y+1/2,-z+1/2,-x+1/2
#22: x+1/2,-y+1/2,-z+1/2
#23: -x+1/2,y+1/2,-z+1/2
#24: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-401-

HOH

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Components

#1: Protein dCTP deaminase / dCTP deaminase / Deoxycytidine triphosphate deaminase


Mass: 17893.748 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus DSM 3638 (archaea) / Gene: dcd, PF1996 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8X251, dCTP deaminase
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 2.26 Å3/Da / Density % sol: 45.63 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 8% TacsimateTM (pH 8.0) , 20% polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 31, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 8395 / % possible obs: 99.82 % / Redundancy: 38.3 % / Biso Wilson estimate: 40.47 Å2 / CC1/2: 0.999 / Net I/σ(I): 93.3
Reflection shellResolution: 2.2→2.24 Å / Num. unique obs: 421 / CC1/2: 0.993

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
PHENIX1.19_4092refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→26.47 Å / SU ML: 0.2187 / Cross valid method: FREE R-VALUE / σ(F): 1.46 / Phase error: 39.2176
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3088 394 4.7 %
Rwork0.2546 7994 -
obs0.257 8388 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.54 Å2
Refinement stepCycle: LAST / Resolution: 2.2→26.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1189 0 21 21 1231
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00361236
X-RAY DIFFRACTIONf_angle_d0.6381674
X-RAY DIFFRACTIONf_chiral_restr0.0553179
X-RAY DIFFRACTIONf_plane_restr0.0026215
X-RAY DIFFRACTIONf_dihedral_angle_d18.5691480
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.520.37841330.33892635X-RAY DIFFRACTION99.96
2.52-3.170.37461330.31992634X-RAY DIFFRACTION100
3.17-26.470.26821280.21272725X-RAY DIFFRACTION99.89

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