5ZYV

Crystal structure of human MGME1 with single strand DNA2 and Ca2+


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.72 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.212 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural insights into DNA degradation by human mitochondrial nuclease MGME1

Yang, C.Wu, R.Liu, H.Chen, Y.Gao, Y.Chen, X.Li, Y.Ma, J.Li, J.Gan, J.

(2018) Nucleic Acids Res. 46: 11075-11088


Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial genome maintenance exonuclease 1
A
254Homo sapiensMutation(s): 1 
Gene Names: MGME1 (C20orf72, DDK1)
EC: 3.1.-.-
Find proteins for Q9BQP7 (Homo sapiens)
Go to Gene View: MGME1
Go to UniProtKB:  Q9BQP7
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(P*CP*AP*AP*CP*AP*AP*T)-3')E15unidentified
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download SDF File 
Download CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.72 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.212 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 81.282α = 90.00
b = 106.151β = 90.00
c = 33.391γ = 90.00
Software Package:
Software NamePurpose
HKL-3000data scaling
HKL-3000data reduction
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2018-05-28 
  • Released Date: 2018-09-19 
  • Deposition Author(s): Yang, C., Gan, J.

Revision History 

  • Version 1.0: 2018-09-19
    Type: Initial release
  • Version 1.1: 2018-10-31
    Type: Data collection, Database references
  • Version 1.2: 2018-11-28
    Type: Data collection, Database references