+Open data
-Basic information
Entry | Database: PDB / ID: 5zyw | ||||||
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Title | The crystal structure of apo-HsMGME1 with Mn2+ | ||||||
Components | Mitochondrial genome maintenance exonuclease 1 | ||||||
Keywords | DNA BINDING PROTEIN / huamnMGME1 / DNA complex / DNA exonuclease / Hydrolase | ||||||
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) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Yang, C. / Gan, J. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2018 Title: Structural insights into DNA degradation by human mitochondrial nuclease MGME1 Authors: Yang, C. / Wu, R. / Liu, H. / Chen, Y. / Gao, Y. / Chen, X. / Li, Y. / Ma, J. / Li, J. / Gan, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5zyw.cif.gz | 66.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5zyw.ent.gz | 45.7 KB | Display | PDB format |
PDBx/mmJSON format | 5zyw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5zyw_validation.pdf.gz | 447.3 KB | Display | wwPDB validaton report |
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Full document | 5zyw_full_validation.pdf.gz | 447.2 KB | Display | |
Data in XML | 5zyw_validation.xml.gz | 11.5 KB | Display | |
Data in CIF | 5zyw_validation.cif.gz | 15.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zy/5zyw ftp://data.pdbj.org/pub/pdb/validation_reports/zy/5zyw | HTTPS FTP |
-Related structure data
Related structure data | 5zytSC 5zyuC 5zyvC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 29517.521 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MGME1, C20orf72, DDK1 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q9BQP7, Hydrolases; Acting on ester bonds | ||||||
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#2: Chemical | #3: Chemical | ChemComp-TLA / | #4: Chemical | ChemComp-GOL / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45.14 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop Details: 0.35 M di-sodium tartrate, 21% PEG 3350 and 0.1 M MnCl2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.9793 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 4, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→30 Å / Num. obs: 14320 / % possible obs: 100 % / Redundancy: 21.6 % / Rmerge(I) obs: 0.105 / Net I/σ(I): 31 |
Reflection shell | Resolution: 2.2→2.28 Å / Num. unique obs: 1388 / CC1/2: 0.799 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5ZYT Resolution: 2.2→29.95 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.909 / SU B: 7.517 / SU ML: 0.186 / Cross valid method: THROUGHOUT / ESU R: 0.324 / ESU R Free: 0.225 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.974 Å2
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Refinement step | Cycle: 1 / Resolution: 2.2→29.95 Å
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Refine LS restraints |
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