3MUT

Crystal Structure of the G20A/C92U mutant c-di-GMP riboswith bound to c-di-GMP

Structural Biology Knowledgebase: 3MUT SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.0 Å
  • R-Value Free: 0.268
  • R-Value Work: 0.233

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3MUT

Classification: RNA BINDING PROTEIN / RNA

Total Structure Weight: 42007.38


Macromolecule Entities
Molecule Chains Length Organism Details
U1 small nuclear ribonucleoprotein A P 98 Homo sapiens Fragment: UNP residues 1-98
Mutation: Y31H, Q36R
Gene Name(s): SNRPA Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
G20A/C92U mutant c-di-GMP riboswitch R 92 synthetic

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
C2E
Query on C2E

R 9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)- 3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro- 2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine- 2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin- 6-one)
c-di-GMP, Cyclic diguanosine monophosphate (Synonym)
C20 H24 N10 O14 P2
PKFDLKSEZWEFGL-MHARETSRSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

R MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
GTP
Query on GTP
R NON-POLYMER C10 H16 N5 O14 P3 G

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.0 Å
  • R-Value Free: 0.268
  • R-Value Work: 0.233
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 49.69 α = 90.00
b = 45.43 β = 95.12
c = 78.93 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2010-05-03
  • Released Date: 2010-08-25
  • Deposition author(s): Strobel, S.A., Smith, K.D.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4