+Open data
-Basic information
Entry | Database: PDB / ID: 8xa9 | ||||||
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Title | Human MGME1 in complex with 5'-overhang DNA | ||||||
Components |
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Keywords | HYDROLASE/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 / mitochondrial DNA replication / mitochondrial genome maintenance / mitochondrial DNA repair / Hydrolases; Acting on ester bonds / mitochondrion Similarity search - Function | ||||||
Biological species | Homo sapiens (human) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 Å | ||||||
Authors | Wu, C.C. / Mao, E.Y.C. | ||||||
Funding support | Taiwan, 1items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8xa9.cif.gz | 127.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8xa9.ent.gz | 86.2 KB | Display | PDB format |
PDBx/mmJSON format | 8xa9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xa/8xa9 ftp://data.pdbj.org/pub/pdb/validation_reports/xa/8xa9 | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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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), Vector: |
-Components
#1: Protein | 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 | Mass: 5535.558 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: DNA chain | Mass: 3304.164 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #4: Chemical | ChemComp-CA / #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.52 Å3/Da / Density % sol: 65.09 % |
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Crystal grow | Temperature: 283 K / Method: vapor diffusion, hanging drop Details: PEG 3350, sodium citrate/citric acid, sodium tribasic, Tris-hydrochloride, sodium chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Jun 9, 2023 |
Radiation | Monochromator: LN2-Cooled, Fixed-Exit Double Crystal Monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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 |
-Processing
Software |
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Refinement | Method 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
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 60.89 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.32→24.46 Å
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Refine LS restraints |
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LS refinement shell |
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