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- PDB-6hde: Structure of Escherichia coli dUTPase Q93H mutant -

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Basic information

Entry
Database: PDB / ID: 6hde
TitleStructure of Escherichia coli dUTPase Q93H mutant
ComponentsDeoxyuridine 5'-triphosphate nucleotidohydrolase
KeywordsHYDROLASE / dUTPase / homotrimer / mutant
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
2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE / Deoxyuridine 5'-triphosphate nucleotidohydrolase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsBenedek, A. / Vertessy, B.G. / Leveles, I.
Funding support Hungary, 1items
OrganizationGrant numberCountry
Hungary
CitationJournal: Biomolecules / Year: 2019
Title: The Role of a Key Amino Acid Position in Species-Specific Proteinaceous dUTPase Inhibition.
Authors: Benedek, A. / Temesvary-Kis, F. / Khatanbaatar, T. / Leveles, I. / Suranyi, E.V. / Szabo, J.E. / Wunderlich, L. / Vertessy, B.G.
History
DepositionAug 17, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 28, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: 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
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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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

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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)50,4129
Polymers48,9383
Non-polymers1,4746
Water2,918162
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15670 Å2
ΔGint-112 kcal/mol
Surface area15430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.200, 66.500, 95.300
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: 16312.633 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: dut, dnaS, sof, b3640, JW3615 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: P06968, 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.: 162 / 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: 2.05 Å3/Da / Density % sol: 39.89 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 0.1 M Tris pH 7.5, 400 mM NaAcetate, 28% PEG 3350, 1.25 mM dUPNPP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS PILATUS3 X 2M / Detector: PIXEL / Date: May 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.8→45.811 Å / Num. obs: 36491 / % possible obs: 99.3 % / Redundancy: 4.5 % / CC1/2: 0.999 / Rrim(I) all: 0.043 / Net I/σ(I): 21.02
Reflection shellResolution: 1.8→1.85 Å

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RN8

1rn8


Resolution: 1.82→45.811 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 0.31 / Phase error: 22.15
RfactorNum. reflection% reflection
Rfree0.2209 1798 4.94 %
Rwork0.1806 --
obs0.1826 36432 99.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.82→45.811 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3232 0 87 162 3481
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073413
X-RAY DIFFRACTIONf_angle_d1.014658
X-RAY DIFFRACTIONf_dihedral_angle_d5.2832487
X-RAY DIFFRACTIONf_chiral_restr0.062531
X-RAY DIFFRACTIONf_plane_restr0.005597
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8198-1.8690.27951320.25192599X-RAY DIFFRACTION98
1.869-1.9240.24751520.22572605X-RAY DIFFRACTION100
1.924-1.98610.24781250.20882654X-RAY DIFFRACTION100
1.9861-2.05710.24281270.19832638X-RAY DIFFRACTION100
2.0571-2.13950.23831460.18992665X-RAY DIFFRACTION100
2.1395-2.23690.2521340.19172641X-RAY DIFFRACTION99
2.2369-2.35480.25721320.19532600X-RAY DIFFRACTION98
2.3548-2.50230.25541310.19642603X-RAY DIFFRACTION97
2.5023-2.69550.2511430.1932670X-RAY DIFFRACTION100
2.6955-2.96670.24521340.18792694X-RAY DIFFRACTION100
2.9667-3.39590.20261430.17022704X-RAY DIFFRACTION100
3.3959-4.27790.17981580.15322713X-RAY DIFFRACTION100
4.2779-45.82590.20391410.17172848X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 11.8597 Å / Origin y: 2.7165 Å / Origin z: 7.1604 Å
111213212223313233
T0.1491 Å20.0048 Å2-0.0016 Å2-0.1449 Å2-0.0135 Å2--0.1303 Å2
L1.0783 °2-0.1491 °20.0715 °2-1.2643 °2-0.2521 °2--0.8191 °2
S0.0299 Å °-0.0337 Å °0.0911 Å °0.0151 Å °-0.023 Å °-0.0103 Å °0.0475 Å °0.0257 Å °-0.0126 Å °
Refinement TLS groupSelection details: all

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