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- PDB-5xd1: Crystal structure of Mycobacterium smegmatis MutT1 in complex wit... -

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Basic information

Entry
Database: PDB / ID: 5xd1
TitleCrystal structure of Mycobacterium smegmatis MutT1 in complex with Ap5A, ATP and magnesium
ComponentsNUDIX family protein
KeywordsHYDROLASE / Nudix enzyme / histidine phosphatase domain / intermolecular interface binding / diadenosine polyphosphates / enzyme action / fluoride inhibition
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
ADENOSINE-5'-PENTAPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / 8-oxo-(d)GTP phosphatase
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsArif, S.M. / Varshney, U. / Vijayan, M.
Citation
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.
#1: Journal: Acta Crystallogr. D Biol. Crystallogr. / 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: Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun.
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
DepositionMar 24, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 9, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 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 / _struct_conn.ptnr2_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NUDIX family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,4927
Polymers38,1531
Non-polymers1,3396
Water6,161342
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area170 Å2
ΔGint-12 kcal/mol
Surface area14070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.210, 83.870, 43.650
Angle α, β, γ (deg.)90.00, 93.24, 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 NUDIX family protein


Mass: 38153.148 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: MSMEG_2390 / Production host: Escherichia coli (E. coli) / Strain (production host): JW0097 / References: UniProt: A0QUZ2

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Non-polymers , 5 types, 348 molecules

#2: Chemical ChemComp-5FA / ADENOSINE-5'-PENTAPHOSPHATE


Type: RNA linking / Mass: 667.141 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H18N5O19P5
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 342 / 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: 2.02 Å3/Da / Density % sol: 39.16 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 8.5
Details: 0.2M sodium acetate trihydrate, 0.1M Tris-HCl pH 8.5, 30%(w/v) PEG4000

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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: Apr 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 1.6→43.58 Å / Num. obs: 38776 / % possible obs: 96.9 % / Redundancy: 4 % / Net I/σ(I): 11
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 3 % / Mean I/σ(I) obs: 2.4 / Num. unique obs: 4771 / % possible all: 81.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
iMOSFLMdata processing
SCALAdata scaling
PHASERphasing
iMOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5gg5

5gg5


Resolution: 1.6→43.58 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.962 / SU B: 2.378 / SU ML: 0.079 / Cross valid method: THROUGHOUT / ESU R: 0.095 / ESU R Free: 0.095 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20903 1936 5 %RANDOM
Rwork0.17423 ---
obs0.17596 36787 96.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 29.976 Å2
Baniso -1Baniso -2Baniso -3
1--0.83 Å2-0 Å21.55 Å2
2---1.71 Å2-0 Å2
3---2.35 Å2
Refinement stepCycle: 1 / Resolution: 1.6→43.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2305 0 79 342 2726
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0192514
X-RAY DIFFRACTIONr_bond_other_d0.0010.022370
X-RAY DIFFRACTIONr_angle_refined_deg1.7871.9923441
X-RAY DIFFRACTIONr_angle_other_deg0.81435446
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2185306
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.56822.348115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.73815411
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8131530
X-RAY DIFFRACTIONr_chiral_restr0.0960.2367
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212816
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02582
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_it2.1182.6881206
X-RAY DIFFRACTIONr_mcbond_other2.1082.6861205
X-RAY DIFFRACTIONr_mcangle_it3.2094.0181518
X-RAY DIFFRACTIONr_mcangle_other3.2084.021519
X-RAY DIFFRACTIONr_scbond_it2.9363.0731308
X-RAY DIFFRACTIONr_scbond_other2.9263.0731308
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.4624.471924
X-RAY DIFFRACTIONr_long_range_B_refined6.6823.5773105
X-RAY DIFFRACTIONr_long_range_B_other6.50822.8072959
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
Rfree0.299 95 -
Rwork0.267 2167 -
obs--76.65 %

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