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- PDB-24ah: Crystal structure of nuclease MYG1 bound to Mn2+ -

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Basic information

Entry
Database: PDB / ID: 24ah
TitleCrystal structure of nuclease MYG1 bound to Mn2+
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
: / MYG1 exonuclease
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.58 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 26, 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)37,0413
Polymers36,9321
Non-polymers1102
Water1,31573
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area280 Å2
ΔGint-12 kcal/mol
Surface area16630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.086, 98.507, 117.174
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-MN / MANGANESE (II) ION


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


Mass: 18.015 Da / Num. of mol.: 73 / 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: 2.74 Å3/Da / Density % sol: 55.08 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: PEG/Ion Screen-G8: 2% v/v Tacsimate, pH 5.0, 0.1 M sodium citrate tribasic dihydrate, pH 5.6, 16% w/v PEG 3350

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Data collection

DiffractionMean temperature: 193 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9786 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 18, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.58→58.59 Å / Num. obs: 13058 / % possible obs: 99.8 % / Redundancy: 6 % / Biso Wilson estimate: 34.64 Å2 / CC1/2: 0.99 / Net I/σ(I): 8.1
Reflection shellResolution: 2.58→2.67 Å / Num. unique obs: 1868 / 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: 2.58→58.59 Å / SU ML: 0.3197 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.9725
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2496 651 5 %
Rwork0.2072 12360 -
obs0.2093 13011 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.13 Å2
Refinement stepCycle: LAST / Resolution: 2.58→58.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2541 0 2 73 2616
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082610
X-RAY DIFFRACTIONf_angle_d0.96113549
X-RAY DIFFRACTIONf_chiral_restr0.0571379
X-RAY DIFFRACTIONf_plane_restr0.0097467
X-RAY DIFFRACTIONf_dihedral_angle_d5.7822353
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.58-2.780.33091270.25762422X-RAY DIFFRACTION99.26
2.78-3.060.29561290.24522447X-RAY DIFFRACTION99.69
3.06-3.50.27771290.22112457X-RAY DIFFRACTION99.81
3.51-4.410.21231310.17922469X-RAY DIFFRACTION99.62
4.42-58.590.22281350.19272565X-RAY DIFFRACTION99.05

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