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- PDB-6m65: Crystal structure of Mycobacterium smegmatis MutT1 in complex wit... -

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Basic information

Entry
Database: PDB / ID: 6m65
TitleCrystal structure of Mycobacterium smegmatis MutT1 in complex with GMPPNP (GDP)
ComponentsHydrolase, NUDIX family protein
KeywordsHYDROLASE / MsMutT1 / Nudix hydrolase / histidine phosphatase domain / Nucleotide pool sanitation enzyme / GMPPNP / Molecular aggregation / plasticity / enzyme action
Function / homology
Function and homology information


8-oxo-(d)GTP phosphatase / diadenosine hexaphosphate hydrolase (ATP-forming) / 8-oxo-dGDP phosphatase / 8-oxo-GDP phosphatase activity / 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: 1.44 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)39,19910
Polymers38,1531
Non-polymers1,0469
Water7,746430
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area840 Å2
ΔGint-13 kcal/mol
Surface area13240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)192.560, 37.110, 44.790
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 , 6 types, 439 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


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


Mass: 18.015 Da / Num. of mol.: 430 / 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: 1.44→43.63 Å / Num. obs: 59223 / % possible obs: 99.7 % / Redundancy: 7.1 % / CC1/2: 0.998 / Rpim(I) all: 0.034 / Rrim(I) all: 0.092 / Rsym value: 0.086 / Net I/av σ(I): 6 / Net I/σ(I): 12.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
1.44-1.5270.75185130.3020.8090.7599.7
1.52-1.617.20.4751.681020.1890.5110.47599.9
1.61-1.727.20.3222.376040.1280.3470.32299.9
1.72-1.867.20.2083.571260.0820.2240.208100
1.86-2.047.20.14565410.0550.150.14100
2.04-2.2870.0996.758120.040.1060.09997.8
2.28-2.637.10.0748.753300.030.080.07499.8
2.63-3.227.10.0698.645200.0270.0740.06999.9
3.22-4.5570.04312.935700.0170.0460.04399.8

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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: 1.44→36.76 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.95 / SU B: 1.361 / SU ML: 0.052 / SU R Cruickshank DPI: 0.0675 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.068 / ESU R Free: 0.071 / Details: Individual isotropic B-factor refinement
RfactorNum. reflection% reflectionSelection details
Rfree0.2148 2985 5 %RANDOM
Rwork0.1814 ---
obs0.1831 56131 99.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 70.52 Å2 / Biso mean: 16.954 Å2 / Biso min: 3.54 Å2
Baniso -1Baniso -2Baniso -3
1--0.62 Å2-0 Å2-0 Å2
2---0.05 Å20 Å2
3---0.66 Å2
Refinement stepCycle: final / Resolution: 1.44→36.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2258 0 64 441 2763
Biso mean--32.91 30.65 -
Num. residues----290
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0132495
X-RAY DIFFRACTIONr_bond_other_d0.0340.0172329
X-RAY DIFFRACTIONr_angle_refined_deg2.081.6823416
X-RAY DIFFRACTIONr_angle_other_deg2.3751.5885377
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4165320
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.28519.862145
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.93915404
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.431530
X-RAY DIFFRACTIONr_chiral_restr0.1080.2317
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022836
X-RAY DIFFRACTIONr_gen_planes_other0.0170.02558
LS refinement shellResolution: 1.44→1.477 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 196 -
Rwork0.289 4122 -
all-4318 -
obs--99.65 %

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