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

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Basic information

Entry
Database: PDB / ID: 5ggd
TitleCrystal structure of Mycobacterium smegmatis MutT1 in complex with phosphate and magnesium ions (excess magnesium, II)
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) / 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
PHOSPHATE ION / 8-oxo-(d)GTP phosphatase
Similarity search - Component
Biological speciesMycobacterium smegmatis str. MC2 155 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hydrolase, NUDIX family protein
B: Hydrolase, NUDIX family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,64210
Polymers76,3062
Non-polymers3368
Water9,206511
1
A: Hydrolase, NUDIX family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,3215
Polymers38,1531
Non-polymers1684
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area160 Å2
ΔGint-13 kcal/mol
Surface area13920 Å2
MethodPISA
2
B: Hydrolase, NUDIX family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,3215
Polymers38,1531
Non-polymers1684
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area160 Å2
ΔGint-13 kcal/mol
Surface area13980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.950, 87.600, 90.530
Angle α, β, γ (deg.)90.00, 100.06, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Hydrolase, NUDIX family protein / / MutT1


Mass: 38153.148 Da / Num. of mol.: 2
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
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 511 / 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: 1.99 Å3/Da / Density % sol: 38.28 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 8.5
Details: 0.2 M magnesium chloride hexahydrate, 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: Oct 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 1.7→44.57 Å / Num. obs: 65728 / % possible obs: 99.9 % / Redundancy: 3.2 % / Net I/σ(I): 6.6
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 1.5 / % 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: 1.7→44.57 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.946 / SU B: 5.06 / SU ML: 0.146 / Cross valid method: THROUGHOUT / ESU R: 0.132 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25863 3313 5.1 %RANDOM
Rwork0.21614 ---
obs0.21834 62029 99.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.036 Å2
Baniso -1Baniso -2Baniso -3
1--1.49 Å2-0 Å22.31 Å2
2---3.21 Å20 Å2
3---3.66 Å2
Refinement stepCycle: LAST / Resolution: 1.7→44.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4556 0 16 511 5083
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0194709
X-RAY DIFFRACTIONr_bond_other_d0.0020.024548
X-RAY DIFFRACTIONr_angle_refined_deg1.9091.9596404
X-RAY DIFFRACTIONr_angle_other_deg0.874310429
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7935584
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.33922.252222
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.01915789
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9821559
X-RAY DIFFRACTIONr_chiral_restr0.1110.2697
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0215316
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021091
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_it2.6812.8152324
X-RAY DIFFRACTIONr_mcbond_other2.6742.8142323
X-RAY DIFFRACTIONr_mcangle_it3.6364.2022903
X-RAY DIFFRACTIONr_mcangle_other3.6364.2032904
X-RAY DIFFRACTIONr_scbond_it3.3153.2372385
X-RAY DIFFRACTIONr_scbond_other3.3033.2352375
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.9064.6873486
X-RAY DIFFRACTIONr_long_range_B_refined6.7324.0635839
X-RAY DIFFRACTIONr_long_range_B_other6.60423.6625642
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.397 230 -
Rwork0.372 4604 -
obs--99.83 %

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