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- PDB-6m69: Crystal structure of Mycobacterium smegmatis MutT1 in complex wit... -

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Basic information

Entry
Database: PDB / ID: 6m69
TitleCrystal structure of Mycobacterium smegmatis MutT1 in complex with GMPPCP (GDP)
ComponentsHydrolase, NUDIX family protein
KeywordsHYDROLASE / MsMutT1 / Nudix hydrolase / histidine phosphatase domain / Nucleotide pool sanitation enzyme / GMPPCP / Molecular aggregation / plasticity / enzyme action
Function / homology
Function and homology information


8-oxo-(d)GTP phosphatase / diadenosine hexaphosphate hydrolase (ATP-forming) / 8-oxo-GDP phosphatase activity / 8-oxo-dGDP phosphatase / 8-oxo-dGDP phosphatase activity / 8-oxo-7,8-dihydroguanosine triphosphate pyrophosphatase activity / DNA replication / DNA repair / metal ion binding
Similarity search - Function
Phosphoglycerate mutase family / Histidine phosphatase superfamily, clade-1 / Histidine phosphatase superfamily (branch 1) / Histidine phosphatase superfamily / NUDIX hydrolase / NUDIX hydrolase, conserved site / Nudix box signature. / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / PYROPHOSPHATE 2- / 8-oxo-(d)GTP phosphatase
Similarity search - Component
Biological speciesMycolicibacterium smegmatis MC2 155 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å
AuthorsRaj, P. / Karthik, S. / Arif, S.M. / Varshney, U. / Vijayan, M.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)BT/PR20529/BRB/10/1525/2016 India
Citation
Journal: Acta Crystallogr D Struct Biol / Year: 2020
Title: Plasticity, ligand conformation and enzyme action of Mycobacterium smegmatis MutT1.
Authors: Raj, P. / Karthik, S. / Arif, S.M. / Varshney, U. / Vijayan, M.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2017
Title: Biochemical and structural studies of Mycobacterium smegmatis MutT1, a sanitization enzyme with unusual modes of association.
Authors: Arif, S.M. / Patil, A.G. / Varshney, U. / Vijayan, M.
#2: Journal: J. Struct. Biol. / Year: 2017
Title: Hydrolysis of diadenosine polyphosphates. Exploration of an additional role of Mycobacterium smegmatis MutT1.
Authors: Arif, S.M. / Varshney, U. / Vijayan, M.
History
DepositionMar 13, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 14, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2020Group: Database references / Category: pdbx_related_exp_data_set
Revision 1.2Nov 29, 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: Hydrolase, NUDIX family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9216
Polymers38,1531
Non-polymers7685
Water6,684371
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area860 Å2
ΔGint-14 kcal/mol
Surface area13160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)192.650, 37.080, 44.800
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Hydrolase, NUDIX family protein


Mass: 38153.148 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium smegmatis MC2 155 (bacteria)
Strain: MC2 155 / Gene: MSMEG_2390 / Production host: Escherichia coli (E. coli) / Strain (production host): JW0097 / References: UniProt: A0QUZ2

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Non-polymers , 5 types, 376 molecules

#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#3: Chemical ChemComp-POP / PYROPHOSPHATE 2-


Mass: 175.959 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O7P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 371 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.1 Å3/Da / Density % sol: 41.6 %
Crystal growTemperature: 298 K / Method: microbatch / pH: 4.6
Details: 0.2 M ammonium acetate, 0.1 M sodium acetate trihydrate, 30% w/v PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.95372 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 1.5→36.74 Å / Num. obs: 52698 / % possible obs: 100 % / Redundancy: 5.4 % / CC1/2: 0.997 / Rpim(I) all: 0.041 / Rrim(I) all: 0.096 / Rsym value: 0.087 / Net I/av σ(I): 5.7 / Net I/σ(I): 9.5
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value
1.5-1.585.40.611.275230.2880.6760.61
1.58-1.685.40.4271.872040.2010.4730.427
1.68-1.795.50.2782.767490.130.3070.278
1.79-1.945.50.2073.163480.0970.2290.207
1.94-2.125.50.1076.857900.050.1180.107
2.12-2.375.40.116552980.0540.1280.116
2.37-2.745.50.083747020.0380.0920.083
2.74-3.355.40.096.440440.0420.10.09
3.35-4.745.30.03815.431730.0180.0420.038

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.21data scaling
PHASERphasing
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GG5

5gg5


Resolution: 1.5→32.82 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.947 / SU B: 1.512 / SU ML: 0.056 / SU R Cruickshank DPI: 0.077 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.077 / ESU R Free: 0.08 / Details: Individual isotropic B-factor refinement
RfactorNum. reflection% reflectionSelection details
Rfree0.2226 2667 5.1 %RANDOM
Rwork0.1884 ---
obs0.1901 49683 99.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 70.16 Å2 / Biso mean: 18.106 Å2 / Biso min: 4.7 Å2
Baniso -1Baniso -2Baniso -3
1--0.72 Å2-0 Å2-0 Å2
2---0.03 Å20 Å2
3---0.75 Å2
Refinement stepCycle: final / Resolution: 1.5→32.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2248 0 46 383 2677
Biso mean--27.9 31.99 -
Num. residues----290
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0132440
X-RAY DIFFRACTIONr_bond_other_d0.0340.0172268
X-RAY DIFFRACTIONr_angle_refined_deg1.9831.6793345
X-RAY DIFFRACTIONr_angle_other_deg2.3671.5885236
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2745314
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.81520139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.72615391
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6391528
X-RAY DIFFRACTIONr_chiral_restr0.110.2313
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022772
X-RAY DIFFRACTIONr_gen_planes_other0.0160.02544
LS refinement shellResolution: 1.5→1.539 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 201 -
Rwork0.256 3623 -
all-3824 -
obs--100 %

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