1JBS

Crystal structure of ribotoxin restrictocin and a 29-mer SRD RNA analog

Structural Biology Knowledgebase: 1JBS SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 0.257
  • R-Value Work: 0.213

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1JBS

Classification: HYDROLASE / RNA

Total Structure Weight: 53026.63


Macromolecule Entities
Molecule Chains Length Organism Details
restrictocin A, B 149 Aspergillus restrictus EC#: 3.1.27 IUBMB
Gene Name(s): ret
Macromolecule Entities
Molecule Chains Length Organism Details
29-mer sarcin/ricin domain RNA analog C, D 29 synthetic

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
K
Query on K

C, D POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 4 Unique
ID Chains Type Formula 2D Diagram Parent
OMC
Query on OMC
C, D RNA LINKING C10 H16 N3 O8 P C
OMG
Query on OMG
C, D RNA LINKING C11 H16 N5 O8 P G
OMU
Query on OMU
C, D RNA LINKING C10 H15 N2 O9 P U
A2M
Query on A2M
C, D RNA LINKING C11 H16 N5 O7 P A

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 0.257
  • R-Value Work: 0.213
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 62.51 α = 90.00
b = 101.86 β = 92.97
c = 41.09 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2001-06-06
  • Released Date: 2001-10-26
  • Deposition author(s): Yang, X., Gerczei, T., Glover, L., Correll, C.C.

Revision History

  • 2013-05-29
    Type: Atom nomenclature | Details: D26 A2M relabel OP3 to OP1 based on connectivity
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Non-polymer description | Details: chemical name/synonym update