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- PDB-5zrc: Structural insights into the catalysis mechanism of M. smegmatis ... -

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Basic information

Entry
Database: PDB / ID: 5zrc
TitleStructural insights into the catalysis mechanism of M. smegmatis antimutator protein MutT2
ComponentsPutative mutator protein MutT2/NUDIX hydrolase
KeywordsHYDROLASE / Nudix hydrolase / MutT / antimutator / CTP pyrophosphorylase
Function / homology
Function and homology information


8-oxo-dGTP diphosphatase / DNA replication / hydrolase activity / DNA repair / metal ion binding
Similarity search - Function
: / NUDIX hydrolase / NUDIX hydrolase, conserved site / Nudix box signature. / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily ...: / NUDIX hydrolase / NUDIX hydrolase, conserved site / Nudix box signature. / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 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)16,1432
Polymers16,0811
Non-polymers621
Water3,009167
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)65.840, 59.870, 31.500
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-456-

HOH

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Components

#1: Protein Putative mutator protein MutT2/NUDIX hydrolase / M. smegmatis 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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 167 / 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: 1.98 Å3/Da / Density % sol: 36.28 %
Crystal growTemperature: 292 K / Method: microbatch
Details: 0.1 M MES monohydrate pH 6.0, 20%(v/v) Jeffamine M-600 pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.8266 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: 0.8266 Å / Relative weight: 1
ReflectionResolution: 1.1→16.46 Å / Num. obs: 49097 / % possible obs: 95.9 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 16
Reflection shellResolution: 1.1→1.16 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.77 / Mean I/σ(I) obs: 3 / Num. unique obs: 6891 / % possible all: 93.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2rrk

2rrk


Resolution: 1.1→16.46 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.964 / SU B: 0.931 / SU ML: 0.02 / Cross valid method: THROUGHOUT / ESU R: 0.029 / ESU R Free: 0.031 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17247 2511 5.1 %RANDOM
Rwork0.14204 ---
obs0.14364 46545 95.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 19.154 Å2
Baniso -1Baniso -2Baniso -3
1-0.53 Å20 Å2-0 Å2
2---0.27 Å20 Å2
3----0.26 Å2
Refinement stepCycle: 1 / Resolution: 1.1→16.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms921 0 4 167 1092
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0191016
X-RAY DIFFRACTIONr_bond_other_d00.02988
X-RAY DIFFRACTIONr_angle_refined_deg1.6431.971394
X-RAY DIFFRACTIONr_angle_other_deg2.01832265
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9535138
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.75622.38142
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.51915159
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.1711514
X-RAY DIFFRACTIONr_chiral_restr0.1160.2158
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0211187
X-RAY DIFFRACTIONr_gen_planes_other0.010.02223
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_it8.0371.368531
X-RAY DIFFRACTIONr_mcbond_other7.9841.361530
X-RAY DIFFRACTIONr_mcangle_it10.5192.037673
X-RAY DIFFRACTIONr_mcangle_other10.5282.04674
X-RAY DIFFRACTIONr_scbond_it4.4621.727485
X-RAY DIFFRACTIONr_scbond_other4.3361.726485
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.2362.456721
X-RAY DIFFRACTIONr_long_range_B_refined22.32515.2271210
X-RAY DIFFRACTIONr_long_range_B_other22.31615.2361211
X-RAY DIFFRACTIONr_rigid_bond_restr13.08432004
X-RAY DIFFRACTIONr_sphericity_free555
X-RAY DIFFRACTIONr_sphericity_bonded31.88552092
LS refinement shellResolution: 1.1→1.129 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.241 161 -
Rwork0.236 3338 -
obs--92.86 %

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