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- PDB-5zrh: M. smegmatis antimutator protein MutT2 in complex with CMP -

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Basic information

Entry
Database: PDB / ID: 5zrh
TitleM. smegmatis antimutator protein MutT2 in complex with CMP
ComponentsPutative mutator protein MutT2/NUDIX hydrolase
KeywordsHYDROLASE / Nudix hydrolase / MutT / antimutator / CTP pyrophosphorylase / CMP
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
CYTIDINE-5'-MONOPHOSPHATE / 8-oxo-dGTP diphosphatase / 8-oxo-dGTP diphosphatase
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.54 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)16,4663
Polymers16,0811
Non-polymers3852
Water3,225179
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area570 Å2
ΔGint-1 kcal/mol
Surface area6260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.640, 59.550, 31.290
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-472-

HOH

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Components

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


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


Mass: 62.068 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C2H6O2
#3: Chemical ChemComp-C5P / CYTIDINE-5'-MONOPHOSPHATE


Mass: 323.197 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N3O8P / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / 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: 1.95 Å3/Da / Density % sol: 35.31 %
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: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54179 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Sep 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 1.54→28.74 Å / Num. obs: 18346 / % possible obs: 98.3 % / Redundancy: 13.1 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 24.6
Reflection shellResolution: 1.54→1.63 Å / Redundancy: 12.1 % / Rmerge(I) obs: 0.586 / Mean I/σ(I) obs: 4.6 / Num. unique obs: 2429 / % possible all: 91.9

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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: 1.54→28.74 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.944 / SU B: 1.408 / SU ML: 0.052 / Cross valid method: THROUGHOUT / ESU R: 0.082 / ESU R Free: 0.086 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20469 938 5.1 %RANDOM
Rwork0.16704 ---
obs0.16899 17376 98.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 15.926 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å2-0 Å20 Å2
2---0.35 Å20 Å2
3---0.44 Å2
Refinement stepCycle: 1 / Resolution: 1.54→28.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms940 0 25 179 1144
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0191061
X-RAY DIFFRACTIONr_bond_other_d00.021016
X-RAY DIFFRACTIONr_angle_refined_deg1.2942.0161459
X-RAY DIFFRACTIONr_angle_other_deg0.60332323
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9385137
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.12221.70741
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.77715157
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4911513
X-RAY DIFFRACTIONr_chiral_restr0.0820.2167
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211206
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02239
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_it1.9891.32536
X-RAY DIFFRACTIONr_mcbond_other1.9761.311535
X-RAY DIFFRACTIONr_mcangle_it3.0431.968677
X-RAY DIFFRACTIONr_mcangle_other3.081.976678
X-RAY DIFFRACTIONr_scbond_it2.7841.593525
X-RAY DIFFRACTIONr_scbond_other2.7841.586517
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.9712.271771
X-RAY DIFFRACTIONr_long_range_B_refined6.61813.0421279
X-RAY DIFFRACTIONr_long_range_B_other6.61613.0441280
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.547→1.587 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 68 -
Rwork0.283 1196 -
obs--94.19 %

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