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- PDB-5zrp: M. smegmatis antimutator protein MutT2 form 3 -

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Basic information

Entry
Database: PDB / ID: 5zrp
TitleM. smegmatis antimutator protein MutT2 form 3
ComponentsPutative mutator protein MutT2/NUDIX hydrolase
KeywordsHYDROLASE / Nudix hydrolase / MutT / antimutator / CTP pyrophosphorylase
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 / nucleotide binding / metal ion binding
Similarity search - Function
: / NUDIX hydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX hydrolase, conserved site / Nudix box signature. / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily ...: / NUDIX hydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX hydrolase, conserved site / Nudix box signature. / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
8-oxo-dGTP diphosphatase / 8-oxo-dGTP diphosphatase
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsSingh, A. / Arif, S.M. / Sang, P.B. / Varshney, U. / Vijayan, M.
CitationJournal: J.Struct.Biol. / Year: 2018
Title: Structural insights into the specificity and catalytic mechanism of mycobacterial nucleotide pool sanitizing enzyme MutT2.
Authors: Singh, A. / Mohammad Arif, S. / Biak Sang, P. / Varshney, U. / Vijayan, M.
History
DepositionApr 24, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 24, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative mutator protein MutT2/NUDIX hydrolase


Theoretical massNumber of molelcules
Total (without water)16,0811
Polymers16,0811
Non-polymers00
Water3,207178
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)36.970, 60.710, 80.380
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Putative mutator protein MutT2/NUDIX hydrolase


Mass: 16081.142 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / Gene: mutT2, MSMEI_5016 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: I7FJF7, UniProt: A0R2K6*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 178 / 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: 2.87 Å3/Da / Density % sol: 56.14 %
Crystal growTemperature: 292 K / Method: microbatch
Details: 0.2 M Ammonium sulfate, 0.1 M Sodium cacodylate trihydrate pH 6.5, 30% w/v PEG 8,000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 31, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.73→33.59 Å / Num. obs: 19279 / % possible obs: 98.5 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.145 / Net I/σ(I): 6.8
Reflection shellResolution: 1.73→1.82 Å / Rmerge(I) obs: 0.441 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 2508 / % possible all: 90.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ZRC

5zrc


Resolution: 1.74→33.59 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.922 / SU B: 3.157 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.102 / ESU R Free: 0.105 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23337 984 5.1 %RANDOM
Rwork0.19643 ---
obs0.19831 18236 99.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 16.617 Å2
Baniso -1Baniso -2Baniso -3
1-0.75 Å20 Å2-0 Å2
2---0.45 Å20 Å2
3----0.3 Å2
Refinement stepCycle: 1 / Resolution: 1.74→33.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms955 0 0 178 1133
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0191013
X-RAY DIFFRACTIONr_bond_other_d00.02980
X-RAY DIFFRACTIONr_angle_refined_deg1.3131.9721387
X-RAY DIFFRACTIONr_angle_other_deg0.64432233
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9725135
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.92221.55645
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.82115156
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2671515
X-RAY DIFFRACTIONr_chiral_restr0.0890.2154
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0211189
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02232
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_it1.8941.373531
X-RAY DIFFRACTIONr_mcbond_other1.8821.372530
X-RAY DIFFRACTIONr_mcangle_it2.832.041669
X-RAY DIFFRACTIONr_mcangle_other2.8282.042670
X-RAY DIFFRACTIONr_scbond_it2.8751.675482
X-RAY DIFFRACTIONr_scbond_other2.8721.675483
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.0932.374719
X-RAY DIFFRACTIONr_long_range_B_refined8.26413.4841242
X-RAY DIFFRACTIONr_long_range_B_other7.50712.1241144
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.736→1.781 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.43 61 -
Rwork0.347 1248 -
obs--95.41 %

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