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- PDB-24bq: Crystal structure of nuclease MYG1(H50A) bound to Mn2+ and dAC -

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Basic information

Entry
Database: PDB / ID: 24bq
TitleCrystal structure of nuclease MYG1(H50A) bound to Mn2+ and dAC
Components
  • DNA (5'-D(P*CP*A)-3')
  • MYG1 exonuclease
KeywordsHYDROLASE/DNA / MYG1 / nuclease / Mn2+ / DHH family / HYDROLASE-DNA complex
Function / homology
Function and homology information


mitochondrial RNA metabolic process / locomotory exploration behavior / mRNA processing / rRNA processing / 3'-5'-RNA exonuclease activity / Hydrolases; Acting on ester bonds / mitochondrial matrix / nucleolus / mitochondrion / nucleoplasm ...mitochondrial RNA metabolic process / locomotory exploration behavior / mRNA processing / rRNA processing / 3'-5'-RNA exonuclease activity / Hydrolases; Acting on ester bonds / mitochondrial matrix / nucleolus / mitochondrion / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Metal-dependent protein hydrolase / Uncharacterised protein family (UPF0160)
Similarity search - Domain/homology
: / DNA / MYG1 exonuclease
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsDing, J. / Lan, C. / Chen, Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Acta Biochim.Biophys.Sin. / Year: 2026
Title: Biochemical and structural studies reveal the substrate specificity and catalytic mechanism of MYG1 as a two-metal ion-dependent 3'→5' exonuclease.
Authors: Lan, C. / Chen, Z. / Wang, G. / Ding, J.
History
DepositionFeb 27, 2026Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 22, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MYG1 exonuclease
C: DNA (5'-D(P*CP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4773
Polymers37,4222
Non-polymers551
Water4,540252
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area830 Å2
ΔGint-9 kcal/mol
Surface area16650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.346, 97.719, 117.066
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein MYG1 exonuclease


Mass: 36864.457 Da / Num. of mol.: 1 / Mutation: H50A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MYG1, C12orf10 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9HB07, Hydrolases; Acting on ester bonds
#2: DNA chain DNA (5'-D(P*CP*A)-3')


Mass: 557.431 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 252 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.69 Å3/Da / Density % sol: 54.24 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.2 M lithium sulfate, 0.1 M Tris, pH 5.5, 25% w/v PEG 3350

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Data collection

DiffractionMean temperature: 193 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL18U / Wavelength: 0.9786 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 22, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.3→29.56 Å / Num. obs: 18081 / % possible obs: 99.1 % / Redundancy: 3.3 % / Biso Wilson estimate: 23.82 Å2 / CC1/2: 0.91 / Net I/σ(I): 3.5
Reflection shellResolution: 2.3→2.38 Å / Num. unique obs: 1705 / CC1/2: 0.75

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-20001.20.1_4487data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→29.56 Å / SU ML: 0.2363 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.3939
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2395 1876 10.39 %
Rwork0.1873 16179 -
obs0.1926 18055 98.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.72 Å2
Refinement stepCycle: LAST / Resolution: 2.3→29.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2531 40 1 252 2824
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00732642
X-RAY DIFFRACTIONf_angle_d0.81063596
X-RAY DIFFRACTIONf_chiral_restr0.0495386
X-RAY DIFFRACTIONf_plane_restr0.0099466
X-RAY DIFFRACTIONf_dihedral_angle_d8.7604368
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.360.27341290.21091190X-RAY DIFFRACTION96.21
2.36-2.430.26761370.19581242X-RAY DIFFRACTION99.14
2.43-2.510.26571440.21181226X-RAY DIFFRACTION98.49
2.51-2.60.25791490.20471212X-RAY DIFFRACTION98.48
2.6-2.710.27591410.20451232X-RAY DIFFRACTION99.64
2.71-2.830.25681710.19931206X-RAY DIFFRACTION99.78
2.83-2.980.26421520.20181244X-RAY DIFFRACTION99.29
2.98-3.160.22761310.18881253X-RAY DIFFRACTION98.93
3.16-3.410.2581470.19121237X-RAY DIFFRACTION99.57
3.41-3.750.20731410.17221267X-RAY DIFFRACTION99.36
3.75-4.290.23141400.16211260X-RAY DIFFRACTION99.15
4.29-5.40.21061530.17011271X-RAY DIFFRACTION99.72
5.4-29.560.22841410.19771339X-RAY DIFFRACTION98.27

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