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- PDB-5ect: Mycobacterium tuberculosis dUTPase G143STOP mutant -

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Basic information

Entry
Database: PDB / ID: 5ect
TitleMycobacterium tuberculosis dUTPase G143STOP mutant
ComponentsDeoxyuridine 5'-triphosphate nucleotidohydrolase
KeywordsHYDROLASE / JELLY-ROLL / TRIMER
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
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.3 Å
AuthorsNagy, G.N. / Leveles, I. / Harmat, V. / Vertessy, G.B.
Funding support Hungary, 3items
OrganizationGrant numberCountry
Hungarian Scientific Research FundNK 84008 Hungary
Hungarian Scientific Research FundK109486 Hungary
Biostruct-X283570 Hungary
CitationJournal: J. Am. Chem. Soc. / Year: 2016
Title: Structural Characterization of Arginine Fingers: Identification of an Arginine Finger for the Pyrophosphatase dUTPases.
Authors: Nagy, G.N. / Suardiaz, R. / Lopata, A. / Ozohanics, O. / Vekey, K. / Brooks, B.R. / Leveles, I. / Toth, J. / Vertessy, B.G. / Rosta, E.
History
DepositionOct 20, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 2, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2016Group: Database references
Revision 1.2Jan 10, 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_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry

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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)17,6915
Polymers16,9851
Non-polymers7064
Water2,288127
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)53,07315
Polymers50,9563
Non-polymers2,11712
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 area14700 Å2
ΔGint-81 kcal/mol
Surface area17290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.780, 54.780, 84.079
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-202-

TRS

21A-202-

TRS

31A-311-

HOH

41A-349-

HOH

51A-402-

HOH

61A-408-

HOH

71A-415-

HOH

81A-419-

HOH

91A-425-

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: 16985.291 Da / Num. of mol.: 1 / Mutation: G143STOP
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: dut, Rv2697c, MTCY05A6.18c / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P9WNS5, dUTP diphosphatase

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Non-polymers , 5 types, 131 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
#3: 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
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 127 / 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: 2.15 Å3/Da / Density % sol: 42.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 1.5 M ammonium sulfate, 0.1M Tris/HCl, 12% glycerol
PH range: 7.5-8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8729 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8729 Å / Relative weight: 1
ReflectionResolution: 1.3→26.05 Å / Num. obs: 34842 / % possible obs: 99.1 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.028 / Net I/σ(I): 21.23
Reflection shellResolution: 1.3→1.344 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 1.95 / % possible all: 99.27

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
XDSdata scaling
Cootmodel building
MOLREPphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 3HZA

3hza


Resolution: 1.3→26.04 Å / Cor.coef. Fo:Fc: 0.986 / Cor.coef. Fo:Fc free: 0.978 / SU B: 2.007 / SU ML: 0.035 / Cross valid method: THROUGHOUT / ESU R: 0.039 / ESU R Free: 0.04 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15679 1813 5.2 %RANDOM
Rwork0.12267 ---
obs0.12441 33008 99.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 21.974 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0 Å2
2---0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: 1 / Resolution: 1.3→26.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1050 0 39 127 1216
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0191126
X-RAY DIFFRACTIONr_bond_other_d0.0010.021115
X-RAY DIFFRACTIONr_angle_refined_deg1.8992.0261541
X-RAY DIFFRACTIONr_angle_other_deg1.24932548
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.725150
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.46921.28239
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.28915167
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4871513
X-RAY DIFFRACTIONr_chiral_restr0.120.2187
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211250
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02235
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.6582.132589
X-RAY DIFFRACTIONr_mcbond_other5.7122.133587
X-RAY DIFFRACTIONr_mcangle_it7.3393.18733
X-RAY DIFFRACTIONr_mcangle_other7.4043.189734
X-RAY DIFFRACTIONr_scbond_it4.5112.2535
X-RAY DIFFRACTIONr_scbond_other4.4952.2535
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.173.228804
X-RAY DIFFRACTIONr_long_range_B_refined7.1417.2511174
X-RAY DIFFRACTIONr_long_range_B_other7.14617.2811175
X-RAY DIFFRACTIONr_rigid_bond_restr5.03832236
X-RAY DIFFRACTIONr_sphericity_free27.47552
X-RAY DIFFRACTIONr_sphericity_bonded16.08652296
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 112 -
Rwork0.269 2459 -
obs--99.27 %

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