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- PDB-7x9n: Crystal structure of MutT-8-oxo-dGTP complex with three Mg2+ ions... -

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Basic information

Entry
Database: PDB / ID: 7x9n
TitleCrystal structure of MutT-8-oxo-dGTP complex with three Mg2+ ions: Reaction using Mg2+
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
8-OXO-2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE / 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: 1.7 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)16,0007
Polymers14,9451
Non-polymers1,0556
Water2,468137
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)38.348, 55.931, 59.079
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 , 1 types, 1 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

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Non-polymers , 5 types, 143 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#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-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
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / 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: 2.12 Å3/Da / Density % sol: 41.97 %
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-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.7→31.63 Å / Num. obs: 14231 / % possible obs: 98.2 % / Redundancy: 4.3 % / Biso Wilson estimate: 13.22 Å2 / Rsym value: 0.123 / Net I/σ(I): 17.1
Reflection shellResolution: 1.7→1.73 Å / Rmerge(I) obs: 0.301 / Num. unique obs: 610

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Processing

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

3a6t


Resolution: 1.7→31.63 Å / SU ML: 0.1732 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 18.924 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2037 697 4.91 %
Rwork0.1602 13486 -
obs0.1623 14183 98.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.44 Å2
Refinement stepCycle: LAST / Resolution: 1.7→31.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1054 0 64 137 1255
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00571182
X-RAY DIFFRACTIONf_angle_d1.34111619
X-RAY DIFFRACTIONf_chiral_restr0.0676161
X-RAY DIFFRACTIONf_plane_restr0.0057204
X-RAY DIFFRACTIONf_dihedral_angle_d16.9083450
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.830.22971240.17852522X-RAY DIFFRACTION93.23
1.83-2.020.2131490.15622664X-RAY DIFFRACTION99.36
2.02-2.310.19761320.15652709X-RAY DIFFRACTION99.44
2.31-2.910.20911460.1682735X-RAY DIFFRACTION99.59
2.91-31.630.19421460.15482856X-RAY DIFFRACTION99.08

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