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- PDB-5zyu: The crystal structure of humanMGME1 with single strand DNA2 -

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Basic information

Entry
Database: PDB / ID: 5zyu
TitleThe crystal structure of humanMGME1 with single strand DNA2
Components
  • DNA (5'-D(P*CP*AP*AP*CP*AP*AP*CP*A)-3')
  • Mitochondrial genome maintenance exonuclease 1
KeywordsDNA BINDING PROTEIN/DNA / huamnMGME1 / DNA complex / DNA exonuclease / DNA BINDING PROTEIN / DNA BINDING PROTEIN-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
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: 1.752 Å
AuthorsYang, C. / Gan, J.
CitationJournal: 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
DepositionMay 28, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 19, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 28, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 23, 2019Group: Data collection / Structure summary / Category: struct / Item: _struct.title
Revision 1.4Aug 28, 2019Group: Data collection / Source and taxonomy / Structure summary
Category: pdbx_entity_src_syn / struct
Item: _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific / _struct.title
Revision 1.5Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: DNA (5'-D(P*CP*AP*AP*CP*AP*AP*CP*A)-3')
C: DNA (5'-D(P*CP*AP*AP*CP*AP*AP*CP*A)-3')
A: Mitochondrial genome maintenance exonuclease 1
B: Mitochondrial genome maintenance exonuclease 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,1935
Polymers68,1014
Non-polymers921
Water9,584532
1
E: DNA (5'-D(P*CP*AP*AP*CP*AP*AP*CP*A)-3')
A: Mitochondrial genome maintenance exonuclease 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1433
Polymers34,0512
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2300 Å2
ΔGint-13 kcal/mol
Surface area14200 Å2
MethodPISA
2
C: DNA (5'-D(P*CP*AP*AP*CP*AP*AP*CP*A)-3')
B: Mitochondrial genome maintenance exonuclease 1


Theoretical massNumber of molelcules
Total (without water)34,0512
Polymers34,0512
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2080 Å2
ΔGint-13 kcal/mol
Surface area14270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.714, 80.714, 79.769
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: DNA chain DNA (5'-D(P*CP*AP*AP*CP*AP*AP*CP*A)-3')


Mass: 4533.020 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Protein Mitochondrial genome maintenance exonuclease 1


Mass: 29517.521 Da / Num. of mol.: 2
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
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 532 / Source method: isolated from a natural source / Formula: H2O

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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: 2.2 Å3/Da / Density % sol: 44.02 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Phosphoric-citric acid pH 4.2 and 20% PEG300

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.75→30 Å / Num. obs: 58405 / % possible obs: 100 % / Redundancy: 9.6 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 16.4
Reflection shellResolution: 1.75→1.81 Å / Num. unique obs: 5780 / CC1/2: 0.624

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ZYT

5zyt


Resolution: 1.752→28.368 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 2.05 / Phase error: 20.5
RfactorNum. reflection% reflection
Rfree0.1996 2912 5.21 %
Rwork0.1735 --
obs0.1749 55877 95.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.752→28.368 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3536 290 6 532 4364
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113955
X-RAY DIFFRACTIONf_angle_d1.0365421
X-RAY DIFFRACTIONf_dihedral_angle_d18.6312310
X-RAY DIFFRACTIONf_chiral_restr0.067607
X-RAY DIFFRACTIONf_plane_restr0.006638
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7521-1.78080.281750.2761202X-RAY DIFFRACTION47
1.7808-1.81150.29811010.24561952X-RAY DIFFRACTION73
1.8115-1.84440.28681120.23682393X-RAY DIFFRACTION91
1.8444-1.87990.26011200.21992636X-RAY DIFFRACTION99
1.8799-1.91830.23811400.21042684X-RAY DIFFRACTION100
1.9183-1.960.25161300.20692633X-RAY DIFFRACTION100
1.96-2.00560.20831260.18572629X-RAY DIFFRACTION100
2.0056-2.05570.21221300.1892674X-RAY DIFFRACTION100
2.0557-2.11130.21611540.17722607X-RAY DIFFRACTION100
2.1113-2.17340.19521340.17072652X-RAY DIFFRACTION100
2.1734-2.24350.20171780.17032593X-RAY DIFFRACTION100
2.2435-2.32360.20371280.16442685X-RAY DIFFRACTION100
2.3236-2.41660.21631600.16852615X-RAY DIFFRACTION100
2.4166-2.52660.17621240.17722665X-RAY DIFFRACTION100
2.5266-2.65970.22821680.17482582X-RAY DIFFRACTION100
2.6597-2.82620.23081580.17792629X-RAY DIFFRACTION100
2.8262-3.04410.18581740.17742618X-RAY DIFFRACTION100
3.0441-3.350.19421630.16732634X-RAY DIFFRACTION100
3.35-3.83380.18881380.15022627X-RAY DIFFRACTION100
3.8338-4.82630.15621570.14162620X-RAY DIFFRACTION100
4.8263-28.37190.18621420.17772635X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -66.4902 Å / Origin y: 21.7835 Å / Origin z: -68.6166 Å
111213212223313233
T0.0743 Å2-0.0305 Å20.0058 Å2-0.113 Å20.0028 Å2--0.1321 Å2
L0.4436 °20.1123 °20.3694 °2-0.3324 °20.2074 °2--0.5332 °2
S-0.0435 Å °-0.0187 Å °0.125 Å °-0.0201 Å °-0.0204 Å °0.0741 Å °-0.0542 Å °-0.0374 Å °0.0567 Å °
Refinement TLS groupSelection details: all

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