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- PDB-5zyv: Crystal structure of human MGME1 with single strand DNA2 and Ca2+ -

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Basic information

Entry
Database: PDB / ID: 5zyv
TitleCrystal structure of human MGME1 with single strand DNA2 and Ca2+
Components
  • DNA (5'-D(P*CP*AP*AP*CP*AP*AP*T)-3')
  • Mitochondrial genome maintenance exonuclease 1
KeywordsDNA BINDING PROTEIN/DNA / humanMGME1 / DNA complex / DNA nuclease / 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
ACETATE ION / DNA / DNA (> 10) / Mitochondrial genome maintenance exonuclease 1
Similarity search - Component
Biological speciesHomo sapiens (human)
unidentified (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.72 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 1.3Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id

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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
E: DNA (5'-D(P*CP*AP*AP*CP*AP*AP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1805
Polymers34,0412
Non-polymers1393
Water23413
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2480 Å2
ΔGint-32 kcal/mol
Surface area10780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.282, 106.151, 33.391
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Mitochondrial genome maintenance exonuclease 1


Mass: 29507.502 Da / Num. of mol.: 1 / Mutation: H180Q
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
#2: DNA chain DNA (5'-D(P*CP*AP*AP*CP*AP*AP*T)-3')


Mass: 4533.020 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) unidentified (others)
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 2.11 Å3/Da / Density % sol: 41.72 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: 0.1M CHESpH 9.5 and 20% PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. obs: 8086 / % possible obs: 97.6 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 17.3
Reflection shellResolution: 2.7→2.8 Å / Num. unique obs: 708 / CC1/2: 0.565

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ZYT

5zyt


Resolution: 2.72→28.3 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / Phase error: 23.75
RfactorNum. reflection% reflection
Rfree0.2539 327 4.52 %
Rwork0.2116 --
obs0.2146 7229 87.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.72→28.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1555 126 6 13 1700
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041733
X-RAY DIFFRACTIONf_angle_d0.6132371
X-RAY DIFFRACTIONf_dihedral_angle_d18.6811004
X-RAY DIFFRACTIONf_chiral_restr0.041267
X-RAY DIFFRACTIONf_plane_restr0.003278
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.80.32591290.25512892X-RAY DIFFRACTION75
2.8-28.26450.23531980.20114010X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -11.1934 Å / Origin y: 20.823 Å / Origin z: -18.2951 Å
111213212223313233
T0.1944 Å20.0154 Å2-0.0692 Å2-0.1871 Å20.0554 Å2--0.0487 Å2
L5.7442 °20.3204 °2-0.4253 °2-4.5409 °2-0.1079 °2--2.0249 °2
S0.24 Å °-0.2568 Å °0.0704 Å °0.4075 Å °-0.266 Å °-0.3154 Å °-0.0485 Å °-0.1205 Å °0.0332 Å °
Refinement TLS groupSelection details: all

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