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Basic information

Entry
Database: PDB / ID: 7yh5
TitleMazG(Mycobacterium tuberculosis)
ComponentsNucleoside triphosphate pyrophosphohydrolase
KeywordsHYDROLASE / MazG / dUTP / nucleoside triphosphate pyrophosphohydrolase
Function / homology
Function and homology information


nucleoside-triphosphate diphosphatase / ATP diphosphatase / ATP diphosphatase activity
Similarity search - Function
NTP pyrophosphohydrolase MazG / : / NTP pyrophosphohydrolase MazG, putative catalytic core / MazG nucleotide pyrophosphohydrolase domain / MazG-like / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Nucleoside triphosphate pyrophosphohydrolase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 2.7 Å
AuthorsLi, J. / Wang, S.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2016YFA0500600 China
CitationJournal: Front Microbiol / Year: 2023
Title: Structural analysis of the housecleaning nucleoside triphosphate pyrophosphohydrolase MazG from Mycobacterium tuberculosis.
Authors: Wang, S. / Gao, B. / Chen, A. / Zhang, Z. / Wang, S. / Lv, L. / Zhao, G. / Li, J.
History
DepositionJul 12, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 19, 2023Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nucleoside triphosphate pyrophosphohydrolase
B: Nucleoside triphosphate pyrophosphohydrolase
C: Nucleoside triphosphate pyrophosphohydrolase
D: Nucleoside triphosphate pyrophosphohydrolase
E: Nucleoside triphosphate pyrophosphohydrolase
F: Nucleoside triphosphate pyrophosphohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,90412
Polymers121,7586
Non-polymers1466
Water63135
1
A: Nucleoside triphosphate pyrophosphohydrolase
B: Nucleoside triphosphate pyrophosphohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6354
Polymers40,5862
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6970 Å2
ΔGint-86 kcal/mol
Surface area16510 Å2
MethodPISA
2
C: Nucleoside triphosphate pyrophosphohydrolase
D: Nucleoside triphosphate pyrophosphohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6354
Polymers40,5862
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6640 Å2
ΔGint-85 kcal/mol
Surface area17190 Å2
MethodPISA
3
E: Nucleoside triphosphate pyrophosphohydrolase
hetero molecules

F: Nucleoside triphosphate pyrophosphohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6354
Polymers40,5862
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_545-y+1/2,x-1/2,z1
Buried area4870 Å2
ΔGint-69 kcal/mol
Surface area15940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.310, 109.310, 242.910
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number90
Space group name H-MP4212
Space group name HallP4ab2ab
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z
#3: y+1/2,-x+1/2,z
#4: x+1/2,-y+1/2,-z
#5: -x+1/2,y+1/2,-z
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
Components on special symmetry positions
IDModelComponents
11B-306-

HOH

21E-304-

HOH

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Components

#1: Protein
Nucleoside triphosphate pyrophosphohydrolase / MazG


Mass: 20292.980 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: ATCC25618/H37Rv / Gene: mazG / Production host: Escherichia coli (E. coli)
References: UniProt: A0A0E7YXB3, nucleoside-triphosphate diphosphatase, ATP diphosphatase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 35 / Source method: isolated from a natural source / Formula: H2O
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: 3.21 Å3/Da / Density % sol: 61.72 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.1 M HEPES pH 7.5, 10% W/V PEG8000, 8% Ethylene glycol

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Data collection

DiffractionMean temperature: 291 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.7→35.86 Å / Num. obs: 41350 / % possible obs: 99.85 % / Redundancy: 2.8 % / Biso Wilson estimate: 87.66 Å2 / CC1/2: 1 / Net I/σ(I): 17.9
Reflection shellResolution: 2.7→2.796 Å / Num. unique obs: 41350 / CC1/2: 1

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 2.7→35.86 Å / SU ML: 0.4227 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.771
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2956 2080 5.03 %
Rwork0.2581 39270 -
obs0.2599 41350 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 90.85 Å2
Refinement stepCycle: LAST / Resolution: 2.7→35.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7077 0 6 35 7118
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00637193
X-RAY DIFFRACTIONf_angle_d0.93869865
X-RAY DIFFRACTIONf_chiral_restr0.05241224
X-RAY DIFFRACTIONf_plane_restr0.00491297
X-RAY DIFFRACTIONf_dihedral_angle_d23.58352499
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.760.38511370.33052567X-RAY DIFFRACTION99.96
2.76-2.830.36571220.32622581X-RAY DIFFRACTION100
2.83-2.910.43481380.33042564X-RAY DIFFRACTION99.96
2.91-2.990.33781360.30842567X-RAY DIFFRACTION99.96
2.99-3.090.35391260.32122597X-RAY DIFFRACTION100
3.09-3.20.33151370.32580X-RAY DIFFRACTION100
3.2-3.330.37521280.29572589X-RAY DIFFRACTION100
3.33-3.480.31691320.28862591X-RAY DIFFRACTION100
3.48-3.660.30161490.26352599X-RAY DIFFRACTION100
3.66-3.890.30481380.25842601X-RAY DIFFRACTION100
3.89-4.190.29261700.2492592X-RAY DIFFRACTION100
4.19-4.610.26941470.23222617X-RAY DIFFRACTION99.93
4.61-5.280.28811530.23272642X-RAY DIFFRACTION100
5.28-6.650.32361220.27472721X-RAY DIFFRACTION99.96
6.65-35.860.25121450.23722862X-RAY DIFFRACTION99.31

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