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- PDB-5zrg: M. smegmatis antimutator protein MutT2 in complex with dCMP -

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Basic information

Entry
Database: PDB / ID: 5zrg
TitleM. smegmatis antimutator protein MutT2 in complex with dCMP
ComponentsPutative mutator protein MutT2/NUDIX hydrolase
KeywordsHYDROLASE / Nudix hydrolase / MutT / antimutator / CTP pyrophosphorylase / dCMP
Function / homology
Function and homology information


8-oxo-dGTP diphosphatase / 8-oxo-7,8-dihydrodeoxyguanosine triphosphate pyrophosphatase activity / DNA replication / hydrolase activity / 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
2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE / 8-oxo-dGTP diphosphatase / 8-oxo-dGTP diphosphatase
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3882
Polymers16,0811
Non-polymers3071
Water2,918162
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area540 Å2
ΔGint2 kcal/mol
Surface area6360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.080, 59.360, 31.360
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-415-

HOH

21A-453-

HOH

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Components

#1: Protein Putative mutator protein MutT2/NUDIX hydrolase / M. smegmatis antimutator protein MutT2


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 BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: I7FJF7, UniProt: A0R2K6*PLUS
#2: Chemical ChemComp-DCM / 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE


Mass: 307.197 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N3O7P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / 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: 1.96 Å3/Da / Density % sol: 35.68 %
Crystal growTemperature: 292 K / Method: microbatch
Details: 0.1 M Imidazole pH 6.5, 1.0 M Sodium acetate trihydrate Cryo: 5% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9762 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 31, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.3→22.08 Å / Num. obs: 30397 / % possible obs: 97.9 % / Redundancy: 7.7 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 11.5
Reflection shellResolution: 1.3→1.37 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.98 / Num. unique obs: 4297 / % possible all: 96.2

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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: 1.3→22.08 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.966 / SU B: 2.074 / SU ML: 0.038 / Cross valid method: THROUGHOUT / ESU R: 0.049 / ESU R Free: 0.05 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18365 1533 5.1 %RANDOM
Rwork0.14232 ---
obs0.14451 28630 96.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 18.793 Å2
Baniso -1Baniso -2Baniso -3
1-1.13 Å20 Å2-0 Å2
2---0.53 Å20 Å2
3----0.6 Å2
Refinement stepCycle: 1 / Resolution: 1.3→22.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms932 0 20 162 1114
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0191041
X-RAY DIFFRACTIONr_bond_other_d0.0010.021002
X-RAY DIFFRACTIONr_angle_refined_deg1.6181.9991437
X-RAY DIFFRACTIONr_angle_other_deg0.85832302
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1685141
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.69823.33339
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.16315158
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.3141511
X-RAY DIFFRACTIONr_chiral_restr0.1120.2166
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0211211
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02221
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_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_it3.0581.522543
X-RAY DIFFRACTIONr_mcbond_other2.9081.517542
X-RAY DIFFRACTIONr_mcangle_it3.8832.281691
X-RAY DIFFRACTIONr_mcangle_other3.9022.285692
X-RAY DIFFRACTIONr_scbond_it4.7211.822498
X-RAY DIFFRACTIONr_scbond_other4.7181.822497
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.32.617746
X-RAY DIFFRACTIONr_long_range_B_refined14.10115.371235
X-RAY DIFFRACTIONr_long_range_B_other10.99113.9161163
X-RAY DIFFRACTIONr_rigid_bond_restr14.70532043
X-RAY DIFFRACTIONr_sphericity_free55.838549
X-RAY DIFFRACTIONr_sphericity_bonded20.8852129
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 89 -
Rwork0.318 1897 -
obs--88.58 %

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