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- PDB-3h6d: Structure of the mycobacterium tuberculosis DUTPase D28N mutant -

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Basic information

Entry
Database: PDB / ID: 3h6d
TitleStructure of the mycobacterium tuberculosis DUTPase D28N mutant
ComponentsDeoxyuridine 5'-triphosphate nucleotidohydrolase
KeywordsHYDROLASE / jelly-roll / 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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsLeveles, I. / Harmat, V. / Nagy, G. / Takacs, E. / Lopata, A. / Toth, J. / Vertessy, B.G.
CitationJournal: Febs Lett. / Year: 2010
Title: Direct contacts between conserved motifs of different subunits provide major contribution to active site organization in human and mycobacterial dUTPases.
Authors: Takacs, E. / Nagy, G. / Leveles, I. / Harmat, V. / Lopata, A. / Toth, J. / Vertessy, B.G.
History
DepositionApr 23, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Refinement description / Version format compliance
Revision 1.2Oct 13, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / diffrn_source ...database_2 / diffrn_source / pdbx_struct_special_symmetry / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 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)18,7275
Polymers17,9911
Non-polymers7364
Water1,60389
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)56,18115
Polymers53,9743
Non-polymers2,20712
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
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.228, 55.228, 83.650
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-203-

TRS

21A-203-

TRS

31A-193-

HOH

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Components

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


Mass: 17991.330 Da / Num. of mol.: 1 / Mutation: D28N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: dut, MT2771, MTCY05A6.18c, Rv2697c / Plasmid: PET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: P0A552, UniProt: P9WNS5*PLUS, dUTP diphosphatase
#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-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 39.91 %
Crystal growTemperature: 298 K / pH: 8.5
Details: 1.45 M Ammonium sulphate, 50 mM Tris, 12% Glycerol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 0.97861
DetectorType: MARMOSAIC 225 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: 1.8→20 Å / Num. obs: 13348 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 3.39 % / Biso Wilson estimate: 26.12 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 14.58
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 2.54 % / Rmerge(I) obs: 0.471 / Mean I/σ(I) obs: 2.41 / % possible all: 99.2

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.5 Å19.16 Å
Translation3.5 Å19.16 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
MOLREPphasing
REFMACrefmac_5.2.0019refinement
PDB_EXTRACT3.005data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2PY4

2py4


Resolution: 1.8→19.16 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.941 / Occupancy max: 1 / Occupancy min: 0.33 / SU B: 5.508 / SU ML: 0.077 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.114 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ARG 140 WAS ASSIGNED TO ELECTRON DENSITY BASED ON STRUCTURAL ALIGNMENT TO THE NATIVE ENZYME.
RfactorNum. reflection% reflectionSelection details
Rfree0.20733 688 5.2 %RANDOM
Rwork0.15765 ---
obs0.1602 12638 99.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 16.224 Å2
Baniso -1Baniso -2Baniso -3
1-0.72 Å20.36 Å20 Å2
2--0.72 Å20 Å2
3----1.09 Å2
Refinement stepCycle: LAST / Resolution: 1.8→19.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1046 0 45 89 1180
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221132
X-RAY DIFFRACTIONr_bond_other_d00.021100
X-RAY DIFFRACTIONr_angle_refined_deg1.7412.0311555
X-RAY DIFFRACTIONr_angle_other_deg2.59232523
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2945151
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.50321.540
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.63515166
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3861513
X-RAY DIFFRACTIONr_chiral_restr0.0910.2186
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211248
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02221
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_refined0.160.259
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1410.226
X-RAY DIFFRACTIONr_symmetry_vdw_other0.280.289
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1970.225
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1381.5734
X-RAY DIFFRACTIONr_mcbond_other0.411.5299
X-RAY DIFFRACTIONr_mcangle_it1.86621183
X-RAY DIFFRACTIONr_scbond_it3.0973398
X-RAY DIFFRACTIONr_scangle_it4.9794.5368
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.248 54 -
Rwork0.229 930 -
obs--99.19 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.89352.9882-2.825611.696-2.47624.8974-0.1145-0.1331-0.23020.1738-0.0584-0.59410.32280.22710.17290.07380.0445-0.04690.06470.02160.12836.21341.2947-26.2716
20.4063-0.1642-0.00190.5944-0.24890.2382-0.0249-0.00850.07060.03060.0083-0.0252-0.04120.02890.01650.0214-0.0064-0.00540.00920.00110.023727.1358-2.7374-0.1098
35.02732.8636-0.24262.3733-1.48442.458-0.18440.2844-0.1336-0.26730.2084-0.05290.2859-0.074-0.0240.0748-0.0201-0.02040.0806-0.01560.030912.9889-28.0427-14.8399
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 22
2X-RAY DIFFRACTION2A23 - 133
3X-RAY DIFFRACTION2A200 - 201
4X-RAY DIFFRACTION3A140

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