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

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Basic information

Entry
Database: PDB / ID: 5zri
TitleM. smegmatis antimutator protein MutT2 in complex with 5m-dCMP
ComponentsPutative mutator protein MutT2/NUDIX hydrolase
KeywordsHYDROLASE / Nudix hydrolase / MutT / antimutator / CTP pyrophosphorylase / CMP / base excision repair
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
Chem-9L3 / 8-oxo-dGTP diphosphatase / 8-oxo-dGTP diphosphatase
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 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 1.2Mar 23, 2022Group: Database references / Derived calculations / Category: database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id
Revision 1.3Nov 22, 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

Downloads & links

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Assembly

Deposited unit
A: Putative mutator protein MutT2/NUDIX hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4123
Polymers16,0811
Non-polymers3312
Water2,936163
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-9 kcal/mol
Surface area6280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.520, 58.840, 31.350
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-459-

HOH

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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 BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: I7FJF7, UniProt: A0R2K6*PLUS
#2: Chemical ChemComp-9L3 / [(2R,3S,5R)-5-(4-azanyl-5-methyl-pyrimidin-1-ium-1-yl)-3-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphate


Mass: 306.232 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N3O6P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / 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: 1.92 Å3/Da / Density % sol: 34.54 %
Crystal growTemperature: 292 K / Method: microbatch
Details: 0.1 M Imidazole pH 6.5, 1.0 M Sodium acetate trihydrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.95372 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 24, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 1.58→29.42 Å / Num. obs: 17324 / % possible obs: 99.7 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 9.1
Reflection shellResolution: 1.58→1.66 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.512 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 2481 / % possible all: 99.2

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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: 1.58→29.42 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.949 / SU B: 1.927 / SU ML: 0.068 / Cross valid method: THROUGHOUT / ESU R: 0.09 / ESU R Free: 0.091 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21116 877 5.1 %RANDOM
Rwork0.17669 ---
obs0.17834 16415 99.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 18.666 Å2
Baniso -1Baniso -2Baniso -3
1-0.69 Å2-0 Å20 Å2
2---1.06 Å20 Å2
3---0.38 Å2
Refinement stepCycle: 1 / Resolution: 1.58→29.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms938 0 21 163 1122
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0191037
X-RAY DIFFRACTIONr_bond_other_d00.02996
X-RAY DIFFRACTIONr_angle_refined_deg0.8361.9861425
X-RAY DIFFRACTIONr_angle_other_deg0.51532273
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0755136
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.44821.77845
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.37115156
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3821514
X-RAY DIFFRACTIONr_chiral_restr0.060.2160
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.0211200
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02239
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_it2.6761.572529
X-RAY DIFFRACTIONr_mcbond_other2.6511.567528
X-RAY DIFFRACTIONr_mcangle_it3.5652.347667
X-RAY DIFFRACTIONr_mcangle_other3.572.35668
X-RAY DIFFRACTIONr_scbond_it3.7671.912508
X-RAY DIFFRACTIONr_scbond_other3.7631.911508
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.2812.738758
X-RAY DIFFRACTIONr_long_range_B_refined7.78315.1921277
X-RAY DIFFRACTIONr_long_range_B_other7.56614.1631194
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.576→1.617 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 79 -
Rwork0.308 1153 -
obs--98.17 %

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