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- PDB-3p48: Structure of the yeast dUTPase DUT1 in complex with dUMPNPP -

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Basic information

Entry
Database: PDB / ID: 3p48
TitleStructure of the yeast dUTPase DUT1 in complex with dUMPNPP
ComponentsDeoxyuridine 5'-triphosphate nucleotidohydrolase
KeywordsHYDROLASE / TRIMER / BETA BARREL / DUMPPNP PYROPHOSPHATASE / PHOSPHOPROTEIN / Structural Genomics / Ontario Centre for Structural Proteomics / OCSP
Function / homology
Function and homology information


pyrimidine deoxyribonucleoside triphosphate catabolic process / dITP catabolic process / dITP diphosphatase activity / Interconversion of nucleotide di- and triphosphates / dUTP catabolic process / dUMP biosynthetic process / dUTP diphosphatase / dUTP diphosphatase activity / magnesium ion binding / nucleus / cytoplasm
Similarity search - Function
Deoxyuridine triphosphate nucleotidohydrolase / Deoxyuridine triphosphatase (dUTPase) / Deoxyuridine 5'-Triphosphate Nucleotidohydrolase; Chain A / dUTPase-like / dUTPase / dUTPase, trimeric / dUTPase-like superfamily / Distorted Sandwich / Mainly Beta
Similarity search - Domain/homology
2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE / Deoxyuridine 5'-triphosphate nucleotidohydrolase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 Å
AuthorsPetit, P. / Singer, A.U. / Evdokimova, E. / Kudritska, M. / Edwards, A.M. / Yakunin, A.F. / Savchenko, A. / Ontario Centre for Structural Proteomics (OCSP)
CitationJournal: Biochem.J. / Year: 2011
Title: Structure and activity of the Saccharomyces cerevisiae dUTP pyrophosphatase DUT1, an essential housekeeping enzyme.
Authors: Tchigvintsev, A. / Singer, A.U. / Flick, R. / Petit, P. / Brown, G. / Evdokimova, E. / Savchenko, A. / Yakunin, A.F.
History
DepositionOct 6, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 27, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 10, 2012Group: Database references
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)47,4449
Polymers45,9703
Non-polymers1,4746
Water7,296405
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10990 Å2
ΔGint-90 kcal/mol
Surface area14380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.784, 58.868, 112.381
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 15323.264 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: DUT1, YBR252W, YBR1705 / Plasmid: PET15B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P33317, dUTP diphosphatase
#2: Chemical ChemComp-DUP / 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE


Mass: 467.157 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C9H16N3O13P3
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 405 / Source method: isolated from a natural source / Formula: H2O

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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: 1.86 Å3/Da / Density % sol: 33.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 30% Jeffamine ED-2001, 0.1M HEPES pH7, 3mM MgCl2, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 24, 2010
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.67→29.43 Å / Num. all: 42235 / Num. obs: 40597 / % possible obs: 96.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.3 % / Rmerge(I) obs: 0.043 / Rsym value: 0.039 / Net I/σ(I): 28.4
Reflection shellResolution: 1.67→1.76 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.239 / Mean I/σ(I) obs: 8.2 / Rsym value: 0.219 / % possible all: 99.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3F4F

3f4f


Resolution: 1.67→28.47 Å / SU ML: 0.16 / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.193 2017 5.02 %
Rwork0.154 --
obs0.156 40218 99 %
all-42235 -
Solvent computationShrinkage radii: 0.89 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.12 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.552 Å2-0 Å20 Å2
2---1.9019 Å2-0 Å2
3---2.4539 Å2
Refinement stepCycle: LAST / Resolution: 1.67→28.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2834 0 87 405 3326
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0172969
X-RAY DIFFRACTIONf_angle_d1.6564052
X-RAY DIFFRACTIONf_dihedral_angle_d17.2991151
X-RAY DIFFRACTIONf_chiral_restr0.115489
X-RAY DIFFRACTIONf_plane_restr0.008501
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.67-1.72970.24051970.17143643X-RAY DIFFRACTION96
1.7297-1.79890.24122170.16783675X-RAY DIFFRACTION97
1.7989-1.88080.22131910.16093735X-RAY DIFFRACTION98
1.8808-1.97990.20111960.14653804X-RAY DIFFRACTION99
1.9799-2.10390.19741680.14443851X-RAY DIFFRACTION100
2.1039-2.26630.2011900.14713842X-RAY DIFFRACTION100
2.2663-2.49430.17822110.13993809X-RAY DIFFRACTION100
2.4943-2.85490.20312100.15583878X-RAY DIFFRACTION100
2.8549-3.59580.1862100.15883902X-RAY DIFFRACTION100
3.5958-28.47770.17522270.15684062X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -16.1363 Å / Origin y: 23.9835 Å / Origin z: -18.7383 Å
111213212223313233
T0.0449 Å20.003 Å2-0.0053 Å2-0.0424 Å20.0126 Å2--0.0382 Å2
L0.4998 °20.0849 °20.1674 °2-0.4653 °20.0202 °2--0.3971 °2
S0.0534 Å °0.0237 Å °-0.0072 Å °0.0415 Å °-0.0234 Å °0.0062 Å °0.0432 Å °0.0516 Å °-0.0244 Å °
Refinement TLS groupSelection details: ALL

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