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- PDB-5zyw: The crystal structure of apo-HsMGME1 with Mn2+ -

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Basic information

Entry
Database: PDB / ID: 5zyw
TitleThe crystal structure of apo-HsMGME1 with Mn2+
ComponentsMitochondrial genome maintenance exonuclease 1
KeywordsDNA 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 / Strand-asynchronous mitochondrial DNA replication / mitochondrial DNA replication / : / mitochondrial DNA repair / Hydrolases; Acting on ester bonds / mitochondrion
Similarity search - Function
Lambda Exonuclease; Chain A - #10 / PD-(D/E)XK endonuclease-like domain, AddAB-type / PD-(D/E)XK nuclease superfamily / Lambda Exonuclease; Chain A / PD-(D/E)XK endonuclease-like domain superfamily / Restriction endonuclease type II-like / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
: / L(+)-TARTARIC ACID / Mitochondrial genome maintenance exonuclease 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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 / Structure summary / Category: struct / Item: _struct.title
Revision 1.5Nov 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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _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_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _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_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mitochondrial genome maintenance exonuclease 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9256
Polymers29,5181
Non-polymers4075
Water1,69394
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area220 Å2
ΔGint-10 kcal/mol
Surface area12560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.997, 67.997, 114.841
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Mitochondrial genome maintenance exonuclease 1


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
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 94 / 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: 2.24 Å3/Da / Density % sol: 45.14 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
Details: 0.35 M di-sodium tartrate, 21% PEG 3350 and 0.1 M MnCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 14320 / % possible obs: 100 % / Redundancy: 21.6 % / Rmerge(I) obs: 0.105 / Net I/σ(I): 31
Reflection shellResolution: 2.2→2.28 Å / Num. unique obs: 1388 / CC1/2: 0.799

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ZYT

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
RfactorNum. reflection% reflectionSelection details
Rfree0.25234 681 5 %RANDOM
Rwork0.22595 ---
obs0.22735 12836 94.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 33.974 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å2-0 Å2-0 Å2
2--0.01 Å2-0 Å2
3----0.03 Å2
Refinement stepCycle: 1 / Resolution: 2.2→29.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1854 0 19 94 1967
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0191913
X-RAY DIFFRACTIONr_bond_other_d0.0020.021790
X-RAY DIFFRACTIONr_angle_refined_deg1.1131.9632594
X-RAY DIFFRACTIONr_angle_other_deg0.84934120
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4345230
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.72624.94185
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.74815324
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.16156
X-RAY DIFFRACTIONr_chiral_restr0.060.2288
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212137
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02433
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2533.482929
X-RAY DIFFRACTIONr_mcbond_other1.2543.484928
X-RAY DIFFRACTIONr_mcangle_it2.265.2061156
X-RAY DIFFRACTIONr_mcangle_other2.2595.2041157
X-RAY DIFFRACTIONr_scbond_it0.9633.501984
X-RAY DIFFRACTIONr_scbond_other0.9633.501984
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.7665.2191439
X-RAY DIFFRACTIONr_long_range_B_refined4.09326.9552200
X-RAY DIFFRACTIONr_long_range_B_other4.00126.9392160
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.201→2.258 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 35 -
Rwork0.269 526 -
obs--55.11 %

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