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- PDB-5gg9: Crystal structure of Mycobacterium smegmatis MutT1 in complex wit... -

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Basic information

Entry
Database: PDB / ID: 5gg9
TitleCrystal structure of Mycobacterium smegmatis MutT1 in complex with 8-oxo-GTP, 8-oxo-GMP and pyrophosphate
ComponentsHydrolase, NUDIX family protein
KeywordsHYDROLASE / 8-oxo-guanine nucleotides / sanitization of nucleotide pool / nudix enzyme / histidine phosphatase domain / binding sites at intermolecular interface / 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) / NUDIX hydrolase / Histidine phosphatase superfamily / 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
Chem-8GM / 8-OXO-GUANOSINE-5'-TRIPHOSPHATE / PYROPHOSPHATE 2- / 8-oxo-(d)GTP phosphatase
Similarity search - Component
Biological speciesMycobacterium smegmatis str. MC2 155 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsArif, S.M. / Patil, A.G. / Varshney, U. / Vijayan, M.
Citation
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.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2012
Title: Crystallization and preliminary X-ray studies of MutT1 (MSMEG_2390) from Mycobacterium smegmatis
Authors: Arif, S.M. / Patil, A.G. / Varshney, U. / Vijayan, M.
History
DepositionJun 15, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 19, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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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)39,2725
Polymers38,1531
Non-polymers1,1194
Water6,089338
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area960 Å2
ΔGint-11 kcal/mol
Surface area14000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.010, 83.950, 44.000
Angle α, β, γ (deg.)90.00, 92.98, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Hydrolase, NUDIX family protein / MutT1


Mass: 38153.148 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis str. 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, 342 molecules

#2: Chemical ChemComp-8GT / 8-OXO-GUANOSINE-5'-TRIPHOSPHATE


Mass: 539.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O15P3
#3: Chemical ChemComp-8GM / [(2R,3S,4R,5R)-5-[2-azanyl-6,8-bis(oxidanylidene)-1,7-dihydropurin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen phosphate / 8-oxoguanosine-5'-phosphate


Mass: 379.220 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O9P
#4: Chemical ChemComp-POP / PYROPHOSPHATE 2-


Mass: 175.959 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O7P2
#5: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 338 / 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: 2.03 Å3/Da / Density % sol: 39.43 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 8.5
Details: 0.2 M sodium acetate trihydrate, 0.1 M TRIS hydrochloride, 30% w/v PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.95372 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 1.6→43.94 Å / Num. obs: 40162 / % possible obs: 99.9 % / Redundancy: 4.5 % / Net I/σ(I): 10.8
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 2.1 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3FJY

3fjy


Resolution: 1.6→43.94 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.96 / SU B: 2.142 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.086 / ESU R Free: 0.09 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20596 2013 5 %RANDOM
Rwork0.16526 ---
obs0.16732 38109 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 28.233 Å2
Baniso -1Baniso -2Baniso -3
1--1.2 Å2-0 Å20.91 Å2
2---0.35 Å20 Å2
3---1.45 Å2
Refinement stepCycle: LAST / Resolution: 1.6→43.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2305 0 68 338 2711
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0192486
X-RAY DIFFRACTIONr_bond_other_d0.0010.022344
X-RAY DIFFRACTIONr_angle_refined_deg1.9771.9893401
X-RAY DIFFRACTIONr_angle_other_deg0.87135385
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5955302
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.44922.281114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.30715406
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7631530
X-RAY DIFFRACTIONr_chiral_restr0.1120.2364
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212784
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02571
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_it2.2222.4891196
X-RAY DIFFRACTIONr_mcbond_other2.2182.4871195
X-RAY DIFFRACTIONr_mcangle_it3.2143.7211502
X-RAY DIFFRACTIONr_mcangle_other3.2143.7241503
X-RAY DIFFRACTIONr_scbond_it3.1522.8981290
X-RAY DIFFRACTIONr_scbond_other3.1612.9021279
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.8574.1921881
X-RAY DIFFRACTIONr_long_range_B_refined6.56322.1043136
X-RAY DIFFRACTIONr_long_range_B_other6.3721.2622969
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 169 -
Rwork0.272 2784 -
obs--99.97 %

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