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- PDB-7ww6: Crystal structure of MutT-8-oxo-dGTP complex: Reaction for 20 min... -

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Basic information

Entry
Database: PDB / ID: 7ww6
TitleCrystal structure of MutT-8-oxo-dGTP complex: Reaction for 20 min in 5 mM Mn2+
Components7,8-dihydro-8-oxoguanine-triphosphatase
KeywordsHYDROLASE / Nudix hydrolase
Function / homology
Function and homology information


8-oxo-dGTP diphosphatase / 8-oxo-GDP phosphatase activity / 8-oxo-dGDP phosphatase activity / 8-oxo-7,8-dihydrodeoxyguanosine triphosphate pyrophosphatase activity / 8-oxo-7,8-dihydroguanosine triphosphate pyrophosphatase activity / DNA replication / DNA repair / metal ion binding
Similarity search - Function
Mutator MutT / : / NUDIX hydrolase / NUDIX hydrolase, conserved site / Nudix box signature. / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily
Similarity search - Domain/homology
sucrose / 8-OXO-2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE / : / 8-oxo-dGTP diphosphatase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.36 Å
AuthorsNakamura, T. / Yamagata, Y.
Funding support Japan, 1items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan) Japan
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2022
Title: Visualization of mutagenic nucleotide processing by Escherichia coli MutT, a Nudix hydrolase.
Authors: Nakamura, T. / Yamagata, Y.
History
DepositionFeb 12, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 1, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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: 7,8-dihydro-8-oxoguanine-triphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0077
Polymers14,9451
Non-polymers1,0626
Water2,540141
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2030 Å2
ΔGint-40 kcal/mol
Surface area6730 Å2
Unit cell
Length a, b, c (Å)38.040, 55.900, 59.240
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein 7,8-dihydro-8-oxoguanine-triphosphatase / 8-oxo-dGTP diphosphatase / 8-oxo-dGTP diphosphatase MutT / Mutator MutT protein / Mutator mutT ...8-oxo-dGTP diphosphatase / 8-oxo-dGTP diphosphatase MutT / Mutator MutT protein / Mutator mutT protein (7 / 8-dihydro-8-oxoguanine-triphosphatase) / Nucleoside triphosphate hydrolase / Nucleoside triphosphate pyrophosphohydrolase / marked preference for dGTP / dGTP-preferring nucleoside triphosphate pyrophosphohydrolase


Mass: 14945.029 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A037YRW7, 8-oxo-dGTP diphosphatase, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#2: Polysaccharide beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose
DescriptorTypeProgram
DFrufb2-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2b_2-5][a2122h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE

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Non-polymers , 5 types, 146 molecules

#3: Chemical ChemComp-8DG / 8-OXO-2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 41.63 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop
Details: potassium sodium tartrate, sodium citrate, ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: Jun 5, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.36→40.66 Å / Num. obs: 27789 / % possible obs: 99.9 % / Redundancy: 6.4 % / Biso Wilson estimate: 11.27 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 16.8
Reflection shellResolution: 1.36→1.4 Å / Rmerge(I) obs: 0.623 / Num. unique obs: 27789

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 3A6T

3a6t


Resolution: 1.36→40.66 Å / SU ML: 0.141 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.2887 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.1845 1390 5 %
Rwork0.1504 26392 -
obs0.1521 27782 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.89 Å2
Refinement stepCycle: LAST / Resolution: 1.36→40.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1055 0 63 141 1259
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00581228
X-RAY DIFFRACTIONf_angle_d1.21371692
X-RAY DIFFRACTIONf_chiral_restr0.087171
X-RAY DIFFRACTIONf_plane_restr0.0048219
X-RAY DIFFRACTIONf_dihedral_angle_d16.6262476
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.36-1.410.321370.2222607X-RAY DIFFRACTION99.93
1.41-1.470.20921360.17332575X-RAY DIFFRACTION99.93
1.47-1.530.18191370.1522598X-RAY DIFFRACTION99.89
1.53-1.610.20541360.13972596X-RAY DIFFRACTION99.93
1.61-1.710.18951380.14082616X-RAY DIFFRACTION99.96
1.71-1.850.19951380.13992621X-RAY DIFFRACTION99.93
1.85-2.030.15491390.13192630X-RAY DIFFRACTION99.93
2.03-2.330.14591400.13462659X-RAY DIFFRACTION100
2.33-2.930.19631410.15872692X-RAY DIFFRACTION99.89
2.93-40.660.18041480.15392798X-RAY DIFFRACTION99.86

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