6DG0 | pdb_00006dg0

MEC-8 C-terminal RRM domain bound to AGCACA

• PDB DOI: https://doi.org/10.2210/pdb6DG0/pdb
• NAKB: 6DG0

• Classification: RNA BINDING PROTEIN/DNA
• Organism(s): Caenorhabditis elegans
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2018-05-16 Released: 2019-08-21 
• Deposition Author(s): Mackereth, C.D., Soufari, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.46 Å
• R-Value Free: 
  0.287 (Depositor), 0.283 (DCC) 
• R-Value Work: 
  0.235 (Depositor), 0.239 (DCC) 
• R-Value Observed: 
  0.238 (Depositor) 

Starting Model: experimental

Literature

Structure of MEC-8 RRM2 in complex with AGCACA

Soufari, H., Mackereth, C.D.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 22.77 kDa 
• Atom Count: 1,620 
• Modeled Residue Count: 180 
• Deposited Residue Count: 188 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mec-8 protein	A, B	88	Caenorhabditis elegans	Mutation(s): 2  Gene Names: mec-8
UniProt
Find proteins for G5ECJ4 (Caenorhabditis elegans) Explore G5ECJ4  Go to UniProtKB:  G5ECJ4

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*GP*CP*AP*CP*A)-3')	C, D	6	Caenorhabditis elegans

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.46 Å
• R-Value Free:  0.287 (Depositor), 0.283 (DCC) 
• R-Value Work:  0.235 (Depositor), 0.239 (DCC) 
• R-Value Observed: 0.238 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.075	α = 90
b = 68.714	β = 122.4
c = 57.531	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-08-21 
Deposition Author(s): Mackereth, C.D., Soufari, H.

Revision History  

• Version 1.0: 2019-08-21
  Type: Initial release
  
• Version 1.1: 2023-10-11
  Changes: Data collection, Database references, Refinement description