[English] 日本語
Yorodumi
- PDB-5zyv: Crystal structure of human MGME1 with single strand DNA2 and Ca2+ -

+
Open data


ID or keywords:

Loading...

-
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 / Strand-asynchronous mitochondrial DNA replication / mitochondrial DNA replication / 5'-flap endonuclease activity / : / mitochondrial DNA repair / Hydrolases; Acting on ester bonds / mitochondrial matrix / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more