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- PDB-8cga: Structure of Mycobacterium tuberculosis dUTPase delta 133A-137S mutant -

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Basic information

Entry
Database: PDB / ID: 8cga
TitleStructure of Mycobacterium tuberculosis dUTPase delta 133A-137S mutant
ComponentsDeoxyuridine 5'-triphosphate nucleotidohydrolase
KeywordsHYDROLASE / dUTP
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 / dUTPase-like / dUTPase / dUTPase, trimeric / dUTPase-like superfamily
Similarity search - Domain/homology
2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE / Deoxyuridine 5'-triphosphate nucleotidohydrolase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsToth, Z.S. / Benedek, A. / Leveles, I. / Vertessy, B.G.
Funding support Hungary, 5items
OrganizationGrant numberCountry
National Research Development and Innovation Office (NKFIH)K119493 Hungary
National Research Development and Innovation Office (NKFIH)K135231 Hungary
National Research Development and Innovation Office (NKFIH)VEKOP-2.3.2-16-2017-00013 Hungary
National Research Development and Innovation Office (NKFIH)NKP-2018-1.2.1-NKP-2018-00005 Hungary
National Research Development and Innovation Office (NKFIH)TKP2021-EGA-02 Hungary
Citation
Journal: Sci Rep / Year: 2024
Title: The homodimerization domain of the Stl repressor is crucial for efficient inhibition of mycobacterial dUTPase.
Authors: Toth, Z.S. / Leveles, I. / Nyiri, K. / Nagy, G.N. / Harmat, V. / Jaroentomeechai, T. / Ozohanics, O. / Miller, R.L. / Alvarez, M.B. / Vertessy, B.G. / Benedek, A.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D.
#2: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
#3: Journal: J.Appl.Crystallogr. / Year: 2007
Title: Phaser crystallographic software.
Authors: McCoy, A.J. / Grosse-Kunstleve, R.W. / Adams, P.D. / Winn, M.D. / Storoni, L.C. / Read, R.J.
History
DepositionFeb 3, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 15, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2024Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)18,3956
Polymers17,5931
Non-polymers8025
Water1,820101
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)55,18418
Polymers52,7793
Non-polymers2,40515
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area14830 Å2
ΔGint-67 kcal/mol
Surface area17650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.249, 55.249, 83.751
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Space group name HallP6c
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/2
#3: y,-x+y,z+1/2
#4: -y,x-y,z
#5: -x+y,-x,z
#6: -x,-y,z+1/2
Components on special symmetry positions
IDModelComponents
11A-202-

SO4

21A-202-

SO4

31A-204-

TRS

41A-204-

TRS

51A-349-

HOH

61A-401-

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: 17592.869 Da / Num. of mol.: 1 / Mutation: delta 133A-137S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: dut, Rv2697c, MTCY05A6.18c / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P9WNS5, dUTP diphosphatase

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Non-polymers , 6 types, 106 molecules

#2: Chemical ChemComp-DUP / 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE


Mass: 467.157 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H16N3O13P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


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


Mass: 18.015 Da / Num. of mol.: 101 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.11 Å3/Da / Density % sol: 41.81 % / Description: rod-like
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 1.5 M Ammonium sulphate, 0.1 M Tris, 12% Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 16, 2021
RadiationMonochromator: Double Crystal Si111 with LN2 closed loop cooling
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.3→47.85 Å / Num. obs: 35602 / % possible obs: 99.96 % / Redundancy: 2 % / Biso Wilson estimate: 9.32 Å2 / Rmerge(I) obs: 0.032 / Rpim(I) all: 0.032 / Rrim(I) all: 0.045 / Net I/σ(I): 14.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) all% possible all
1.3-1.350.2932.735810.2940.415100
1.35-1.40.2393.335160.2390.33799.9
1.4-1.460.194.135410.190.29699.9
1.46-1.540.1435.335640.1430.203100
1.54-1.640.1057.535280.1050.149100
1.64-1.760.0741035630.0740.105
1.76-1.940.04415.335360.0440.062
1.94-2.220.02522.635920.0250.036100
2.22-2.80.01928.335680.0190.026100
2.8-47.850.0154236130.0150.021100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.19.2_4158-000refinement
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2PY4

2py4


Resolution: 1.3→47.85 Å / SU ML: 0.0939 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.71
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1701 1706 4.79 %
Rwork0.141 33895 -
obs0.1424 35601 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 13.7 Å2
Refinement stepCycle: LAST / Resolution: 1.3→47.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1047 0 48 101 1196
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00681144
X-RAY DIFFRACTIONf_angle_d1.03171567
X-RAY DIFFRACTIONf_chiral_restr0.0839188
X-RAY DIFFRACTIONf_plane_restr0.012200
X-RAY DIFFRACTIONf_dihedral_angle_d10.4192187
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.340.21091400.15792827X-RAY DIFFRACTION100
1.34-1.380.18921650.1622797X-RAY DIFFRACTION100
1.38-1.430.21261320.15822827X-RAY DIFFRACTION100
1.43-1.490.8971240.14852814X-RAY DIFFRACTION100
1.49-1.560.19471700.12482784X-RAY DIFFRACTION100
1.56-1.640.17411580.12412792X-RAY DIFFRACTION100
1.64-1.740.16871380.12062835X-RAY DIFFRACTION100
1.74-1.870.13461010.12192866X-RAY DIFFRACTION100
1.87-2.060.16121270.11482828X-RAY DIFFRACTION100
2.06-2.360.13031580.13072815X-RAY DIFFRACTION100
2.36-2.980.18271280.1482855X-RAY DIFFRACTION100
2.98-47.850.17331650.15982855X-RAY DIFFRACTION100

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