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- PDB-7x9j: Crystal structure of MutT-8-oxo-dGTP complex: Reaction for 24 hr ... -

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Basic information

Entry
Database: PDB / ID: 7x9j
TitleCrystal structure of MutT-8-oxo-dGTP complex: Reaction for 24 hr using 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'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE / : / 8-oxo-dGTP diphosphatase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.98 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
DepositionMar 15, 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)15,8256
Polymers14,9451
Non-polymers8805
Water2,396133
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.130, 55.980, 59.198
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 (E. coli)
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, 137 molecules

#3: Chemical ChemComp-8OG / 8-OXO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE / 8-OXO-7,8-DIHYDRO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE


Type: DNA linking / Mass: 363.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O8P / 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-MN / MANGANESE (II) ION


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


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / 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: 41.81 %
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: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Mar 28, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.98→26.17 Å / Num. obs: 9248 / % possible obs: 99.3 % / Redundancy: 6.8 % / Biso Wilson estimate: 13.7 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 52.7
Reflection shellResolution: 1.98→2.05 Å / Rmerge(I) obs: 0.133 / Num. unique obs: 809

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-2000data reduction
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 3A6T

3a6t


Resolution: 1.98→26.17 Å / SU ML: 0.1515 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.9544 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2124 461 5 %
Rwork0.1518 8755 -
obs0.1549 9216 99.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 15.95 Å2
Refinement stepCycle: LAST / Resolution: 1.98→26.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1055 0 54 133 1242
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00561142
X-RAY DIFFRACTIONf_angle_d1.14871555
X-RAY DIFFRACTIONf_chiral_restr0.0592161
X-RAY DIFFRACTIONf_plane_restr0.0046196
X-RAY DIFFRACTIONf_dihedral_angle_d14.7646434
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.98-2.050.22561490.13422833X-RAY DIFFRACTION98.42
2.05-2.850.24671520.16032884X-RAY DIFFRACTION99.67
2.85-26.170.18741600.15463038X-RAY DIFFRACTION99.88

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