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- PDB-1dup: DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDO HYDROLASE (D-UTPASE) -

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Basic information

Entry
Database: PDB / ID: 1dup
TitleDEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDO HYDROLASE (D-UTPASE)
ComponentsDEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE
KeywordsHYDROLASE / NUCLEOTIDE METABOLISM
Function / homology
Function and homology information


dUTP catabolic process / dUMP biosynthetic process / dUTP diphosphatase / dUTP diphosphatase activity / protein homotrimerization / magnesium ion binding / protein-containing complex / identical protein binding / cytosol
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
Deoxyuridine 5'-triphosphate nucleotidohydrolase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsDauter, Z. / Wilson, K.S. / Larsson, G. / Nyman, P.O. / Cedergren, E.
CitationJournal: Nature / Year: 1992
Title: Crystal structure of a dUTPase.
Authors: Cedergren-Zeppezauer, E.S. / Larsson, G. / Nyman, P.O. / Dauter, Z. / Wilson, K.S.
History
DepositionSep 1, 1995Processing site: BNL
Revision 1.0Nov 14, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 29, 2017Group: Advisory / Category: pdbx_unobs_or_zero_occ_atoms
Revision 1.4Feb 7, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE


Theoretical massNumber of molelcules
Total (without water)16,3031
Polymers16,3031
Non-polymers00
Water2,216123
1
A: DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE

A: DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE

A: DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE


Theoretical massNumber of molelcules
Total (without water)48,9083
Polymers48,9083
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area9890 Å2
ΔGint-73 kcal/mol
Surface area16440 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)86.610, 86.610, 62.270
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-188-

HOH

21A-231-

HOH

DetailsTHE STRUCTURE IS BUILT-UP OF TIGHT TRIMERS AROUND THE CRYSTALLOGRAPHIC THREE-FOLD AXIS. MTRIX THE TRANSFORMATIONS PRESENTED ON MTRIX RECORDS BELOW DESCRIBE NON-CRYSTALLOGRAPHIC RELATIONSHIPS AMONG THE VARIOUS DOMAINS IN THIS ENTRY. APPLYING THE APPROPRIATE MTRIX TRANSFORMATION TO THE RESIDUES LISTED FIRST WILL YIELD APPROXIMATE COORDINATES FOR THE RESIDUES LISTED SECOND. APPLIED TO TRANSFORMED TO MTRIX RESIDUES RESIDUES RMSD M1 A 1 .. A 136 1 .. 136 M2 A 1 .. A 136 1 .. 136 THESE TRANSFORMATIONS WILL YIELD THE COORDINATES FOR THE TWO OTHER SUBUNITS OF THE TRIMER.

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Components

#1: Protein DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE / D-UTPASE


Mass: 16302.615 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Cell line: S2 / References: UniProt: P06968, dUTP diphosphatase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / Source method: isolated from a natural source / Formula: H2O
Compound detailsSECONDARY STRUCTURE BOUNDARIES HAVE BEEN DETERMINED USING SS PROGRAM (V.S.LAMZIN, EMBL HAMBURG) AS ...SECONDARY STRUCTURE BOUNDARIES HAVE BEEN DETERMINED USING SS PROGRAM (V.S.LAMZIN, EMBL HAMBURG) AS DESCRIBED IN V.S.LAMZIN,Z.DAUTER,V.O.POPOV,E.H.HARUTYUNYAN,K.S.WILSON J.MOL.BIOL. (1994) V.236, 759-785 STRAND 2 IN SHEET S2 IS SPLIT INTO S2A (GLY 114 - ILE 117).

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.76 Å3/Da / Density % sol: 55.36 %
Crystal grow
*PLUS
pH: 4.2 / Method: other
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
20.05 M11MgCl2
30.45 Mpyrophosphate11
1PEG800011
4succinate11

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.9 Å / Num. obs: 13640 / % possible obs: 96 % / Rmerge(I) obs: 0.069

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Processing

Software
NameClassification
ARP/wARPmodel building
PROLSQrefinement
RefinementResolution: 1.9→10 Å / σ(F): 0 /
RfactorNum. reflection% reflection
obs0.15 13597 98.9 %
Refinement stepCycle: LAST / Resolution: 1.9→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1027 0 0 123 1150
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0170.02
X-RAY DIFFRACTIONp_angle_d0.0440.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0470.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.42
X-RAY DIFFRACTIONp_mcangle_it3.43
X-RAY DIFFRACTIONp_scbond_it5.64
X-RAY DIFFRACTIONp_scangle_it7.85
X-RAY DIFFRACTIONp_plane_restr0.0150.02
X-RAY DIFFRACTIONp_chiral_restr0.180.15
X-RAY DIFFRACTIONp_singtor_nbd0.1860.3
X-RAY DIFFRACTIONp_multtor_nbd0.2630.3
X-RAY DIFFRACTIONp_xhyhbond_nbd0.1940.3
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor2.83
X-RAY DIFFRACTIONp_staggered_tor15.615
X-RAY DIFFRACTIONp_orthonormal_tor31.720
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor

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