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- PDB-3hza: Crystal structure of dUTPase H145W mutant -

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Basic information

Entry
Database: PDB / ID: 3hza
TitleCrystal structure of dUTPase H145W mutant
ComponentsDeoxyuridine 5'-triphosphate nucleotidohydrolase
KeywordsHYDROLASE / jelly roll / domain swapping / Nucleotide metabolism
Function / homology
Function and homology information


dUTP metabolic process / dUTP catabolic process / dUMP biosynthetic process / dUTP diphosphatase / dUTP diphosphatase activity / magnesium ion binding
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 / Deoxyuridine 5'-triphosphate nucleotidohydrolase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.2 Å
AuthorsLeveles, I. / Harmat, V. / Pecsi, I. / Toth, J. / Vertessy, B.G.
CitationJournal: Nucleic Acids Res. / Year: 2010
Title: Aromatic stacking between nucleobase and enzyme promotes phosphate ester hydrolysis in dUTPase.
Authors: Pecsi, I. / Leveles, I. / Harmat, V. / Vertessy, B.G. / Toth, J.
History
DepositionJun 23, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Nov 1, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.3Oct 13, 2021Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: database_2 / diffrn_source ...database_2 / diffrn_source / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_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_conn.ptnr2_symmetry / _struct_conn_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Deoxyuridine 5'-triphosphate nucleotidohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8386
Polymers18,0401
Non-polymers7985
Water3,531196
1
A: Deoxyuridine 5'-triphosphate nucleotidohydrolase
hetero molecules

A: Deoxyuridine 5'-triphosphate nucleotidohydrolase
hetero molecules

A: Deoxyuridine 5'-triphosphate nucleotidohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,51518
Polymers54,1213
Non-polymers2,39315
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area13840 Å2
ΔGint-61.8 kcal/mol
Surface area19650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.058, 55.058, 83.793
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-204-

TRS

21A-204-

TRS

31A-406-

HOH

41A-437-

HOH

51A-440-

HOH

61A-447-

HOH

71A-467-

HOH

81A-477-

HOH

91A-478-

HOH

101A-494-

HOH

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 18040.377 Da / Num. of mol.: 1 / Mutation: H145W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: dut, Rv2697c, MT2771, MTCY05A6.18c / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P0A552, UniProt: P9WNS5*PLUS, dUTP diphosphatase

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Non-polymers , 5 types, 201 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-DUP / 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE


Mass: 467.157 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H16N3O13P3
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 196 / 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: 2.03 Å3/Da / Density % sol: 39.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.3 M Ammonium sulfate, 50 mM Tris-HCl, 12 % Glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 0.97861 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 12, 2008 / Details: Mirrors
RadiationMonochromator: Double crystal Si[111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97861 Å / Relative weight: 1
ReflectionResolution: 1.2→20 Å / Num. obs: 42370 / % possible obs: 94.2 % / Observed criterion σ(I): -3 / Redundancy: 3.73 % / Biso Wilson estimate: 16.422 Å2 / Rsym value: 0.039 / Net I/σ(I): 18.4
Reflection shellResolution: 1.2→1.23 Å / Redundancy: 1.467 % / Mean I/σ(I) obs: 2.02 / Num. unique all: 2286 / Rsym value: 0.472 / % possible all: 68.9

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Processing

Software
NameVersionClassification
MAR345CCDdata collection
MOLREPphasing
SHELXL-97refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 2PY4

2py4


Resolution: 1.2→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: 1. Used CGLS procedure. 2. Atomic anisotropic B values were refined for non-hydrogen atoms. 3. Hydrogen atoms were generated in the riding positions.
RfactorNum. reflectionSelection details
Rfree0.1593 2252 RANDOM
Rwork0.1167 --
obs0.1167 42364 -
all-42364 -
Refinement stepCycle: LAST / Resolution: 1.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1162 0 45 196 1403
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.061
X-RAY DIFFRACTIONs_bond_d0.012
X-RAY DIFFRACTIONs_angle_d0.029
X-RAY DIFFRACTIONs_zero_chiral_vol0.07
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.066
X-RAY DIFFRACTIONs_from_restr_planes0.407
X-RAY DIFFRACTIONs_approx_iso_adps0.078
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.046

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