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- PDB-24bs: Crystal structure of nuclease MYG1 bound to Mn2+ and dAMP -

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Basic information

Entry
Database: PDB / ID: 24bs
TitleCrystal structure of nuclease MYG1 bound to Mn2+ and dAMP
ComponentsMYG1 exonuclease
KeywordsHYDROLASE / MYG1 / nuclease / Mn2+ / DHH family
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
2'-DEOXYADENOSINE-5'-MONOPHOSPHATE / : / MYG1 exonuclease
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3734
Polymers36,9321
Non-polymers4413
Water6,305350
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area730 Å2
ΔGint-19 kcal/mol
Surface area16430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.698, 97.870, 116.897
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: 36931.527 Da / Num. of mol.: 1
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: Chemical ChemComp-D5M / 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE


Mass: 331.222 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O6P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 350 / 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: 2.7 Å3/Da / Density % sol: 54.43 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.1 M magnesium acetate, 0.1 M sodium cacodylate, pH 6.5, 15% w/v PEG 6000

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Data collection

DiffractionMean temperature: 193 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.9791 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 14, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2→25.98 Å / Num. obs: 26717 / % possible obs: 97.7 % / Redundancy: 11.4 % / Biso Wilson estimate: 22.12 Å2 / CC1/2: 0.99 / Net I/σ(I): 13.7
Reflection shellResolution: 2→2.07 Å / Num. unique obs: 1577 / CC1/2: 0.81

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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→25.98 Å / SU ML: 0.2075 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.7531
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1995 1999 7.5 %
Rwork0.1692 24665 -
obs0.1715 26664 97.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.57 Å2
Refinement stepCycle: LAST / Resolution: 2→25.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2541 0 24 350 2915
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00662634
X-RAY DIFFRACTIONf_angle_d0.80363585
X-RAY DIFFRACTIONf_chiral_restr0.0518383
X-RAY DIFFRACTIONf_plane_restr0.0093468
X-RAY DIFFRACTIONf_dihedral_angle_d14.6439949
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.29131120.2181398X-RAY DIFFRACTION78.48
2.05-2.110.26871300.2081602X-RAY DIFFRACTION90.49
2.11-2.170.25021440.19131762X-RAY DIFFRACTION98.96
2.17-2.240.2211440.18311790X-RAY DIFFRACTION99.54
2.24-2.320.22881440.1861772X-RAY DIFFRACTION99.22
2.32-2.410.22621450.17451773X-RAY DIFFRACTION99.43
2.41-2.520.21521440.17181791X-RAY DIFFRACTION99.59
2.52-2.650.22851450.17961788X-RAY DIFFRACTION99.64
2.65-2.820.19851450.18031786X-RAY DIFFRACTION99.69
2.82-3.040.21271470.16511816X-RAY DIFFRACTION99.95
3.04-3.340.1651480.16051821X-RAY DIFFRACTION99.8
3.34-3.820.20311470.15051808X-RAY DIFFRACTION99.95
3.82-4.810.16111480.14341838X-RAY DIFFRACTION99.95
4.81-25.980.17491560.17791920X-RAY DIFFRACTION99.52

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