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- PDB-8xa9: Human MGME1 in complex with 5'-overhang DNA -

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Basic information

Entry
Database: PDB / ID: 8xa9
TitleHuman MGME1 in complex with 5'-overhang DNA
Components
  • DNA (11-MER)
  • DNA (18-MER)
  • Mitochondrial genome maintenance exonuclease 1
KeywordsHYDROLASE/DNA / Exonuclease / HYDROLASE / HYDROLASE-DNA complex
Function / homology
Function and homology information


single-stranded DNA exodeoxyribonuclease activity / single-stranded DNA 5'-3' DNA exonuclease activity / Strand-asynchronous mitochondrial DNA replication / mitochondrial DNA replication / 5'-flap endonuclease activity / : / mitochondrial DNA repair / Hydrolases; Acting on ester bonds / mitochondrial matrix / mitochondrion
Similarity search - Function
PD-(D/E)XK endonuclease-like domain, AddAB-type / PD-(D/E)XK nuclease superfamily / PD-(D/E)XK endonuclease-like domain superfamily / Restriction endonuclease type II-like
Similarity search - Domain/homology
DNA / DNA (> 10) / Mitochondrial genome maintenance exonuclease 1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 Å
AuthorsWu, C.C. / Mao, E.Y.C.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
National Science Council (NSC, Taiwan)NSTC 112-2636-B-006-005 - Taiwan
CitationJournal: Nucleic Acids Res. / Year: 2024
Title: Structural basis of how MGME1 processes DNA 5' ends to maintain mitochondrial genome integrity.
Authors: Mao, E.Y.C. / Yen, H.Y. / Wu, C.C.
History
DepositionDec 3, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 20, 2024Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mitochondrial genome maintenance exonuclease 1
B: Mitochondrial genome maintenance exonuclease 1
C: DNA (18-MER)
D: DNA (11-MER)
E: DNA (18-MER)
F: DNA (11-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,07210
Polymers75,9126
Non-polymers1604
Water1,26170
1
A: Mitochondrial genome maintenance exonuclease 1
E: DNA (18-MER)
F: DNA (11-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0365
Polymers37,9563
Non-polymers802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2810 Å2
ΔGint-52 kcal/mol
Surface area13900 Å2
MethodPISA
2
B: Mitochondrial genome maintenance exonuclease 1
C: DNA (18-MER)
D: DNA (11-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0365
Polymers37,9563
Non-polymers802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3150 Å2
ΔGint-51 kcal/mol
Surface area14650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)180.756, 56.193, 114.445
Angle α, β, γ (deg.)90.000, 113.020, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS oper: (Code: givenMatrix: (0.692943046204, 0.00894448967821, 0.720936842464), (0.00932901340299, -0.999950568881, 0.0034393755881), (0.720931969208, 0.004342338069, -0.692992236518)Vector: -8. ...NCS oper: (Code: given
Matrix: (0.692943046204, 0.00894448967821, 0.720936842464), (0.00932901340299, -0.999950568881, 0.0034393755881), (0.720931969208, 0.004342338069, -0.692992236518)
Vector: -8.52466571364, 7.47898508641, 20.1462812978)

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Components

#1: Protein Mitochondrial genome maintenance exonuclease 1


Mass: 29116.125 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MGME1 / Plasmid: pSol SUMO / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: Q9BQP7
#2: DNA chain DNA (18-MER)


Mass: 5535.558 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (11-MER)


Mass: 3304.164 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.52 Å3/Da / Density % sol: 65.09 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop
Details: PEG 3350, sodium citrate/citric acid, sodium tribasic, Tris-hydrochloride, sodium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jun 9, 2023
RadiationMonochromator: LN2-Cooled, Fixed-Exit Double Crystal Monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.32→30 Å / Num. obs: 43737 / % possible obs: 96.4 % / Redundancy: 3.3 % / Biso Wilson estimate: 48.47 Å2 / Rpim(I) all: 0.035 / Rrim(I) all: 0.066 / Χ2: 0.998 / Net I/σ(I): 13.6
Reflection shellResolution: 2.35→2.4 Å / Redundancy: 3.1 % / Num. unique obs: 2393 / CC1/2: 0.925 / CC star: 0.98 / Rpim(I) all: 0.335 / Rrim(I) all: 0.608 / Χ2: 0.999 / % possible all: 95.5

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
Cootmodel building
Blu-Icedata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.32→24.46 Å / SU ML: 0.2817 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.0088
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.278 2162 4.95 %
Rwork0.258 41541 -
obs0.259 43703 94.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 60.89 Å2
Refinement stepCycle: LAST / Resolution: 2.32→24.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3329 561 4 70 3964
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044064
X-RAY DIFFRACTIONf_angle_d0.61555648
X-RAY DIFFRACTIONf_chiral_restr0.0387641
X-RAY DIFFRACTIONf_plane_restr0.0036623
X-RAY DIFFRACTIONf_dihedral_angle_d19.58471475
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.32-2.370.3631020.3522007X-RAY DIFFRACTION69.72
2.37-2.430.32721360.31792773X-RAY DIFFRACTION95.25
2.43-2.50.33331540.3192748X-RAY DIFFRACTION95.09
2.5-2.570.31481480.30442744X-RAY DIFFRACTION94.32
2.57-2.660.30741470.29482756X-RAY DIFFRACTION95.02
2.66-2.750.36371400.30022750X-RAY DIFFRACTION94.63
2.75-2.860.30221440.29832791X-RAY DIFFRACTION95.66
2.86-2.990.32081560.31132783X-RAY DIFFRACTION96.42
2.99-3.150.32791410.29392836X-RAY DIFFRACTION96.5
3.15-3.340.32771200.2822861X-RAY DIFFRACTION96.82
3.34-3.60.25631370.26212825X-RAY DIFFRACTION96.64
3.6-3.960.22941570.23552885X-RAY DIFFRACTION98
3.96-4.530.21421390.20842930X-RAY DIFFRACTION98.94
4.53-5.70.24851710.22492918X-RAY DIFFRACTION99.2
5.7-24.460.31021700.25262934X-RAY DIFFRACTION96.82

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