1OJ8 | pdb_00001oj8

Novel and retro Binding Modes in Cytotoxic Ribonucleases from Rana catesbeiana of Two Crystal Structures Complexed with d(ApCpGpA) and (2',5'CpG)

• PDB DOI: https://doi.org/10.2210/pdb1OJ8/pdb
• NAKB: 1OJ8

• Classification: HYDROLASE
• Organism(s): Aquarana catesbeiana
• Mutation(s): No 


• Deposited: 2003-07-07 Released: 2004-07-15 
• Deposition Author(s): Tsai, C.-J., Liu, J.-H., Liao, Y.-D., Chen, L.-Y., Cheng, P.-T., Sun, Y.-J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.273 (Depositor), 0.278 (DCC) 
• R-Value Work: 
  0.229 (Depositor), 0.235 (DCC) 
• R-Value Observed: 
  0.229 (Depositor) 

Starting Model: experimental

Literature

Retro and Novel Binding Modes in Cytotoxic Ribonucleases from Rana Catesbeiana of Two Crystal Structures Complexed with (2',5'Cpg) and D(Apcpgpa)

Tsai, C.-J., Liu, J.-H., Liao, Y.-D., Chen, L.-Y., Cheng, P.-T., Sun, Y.-J.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content 

• Total Structure Weight: 13.58 kDa 
• Atom Count: 1,162 
• Modeled Residue Count: 109 
• Deposited Residue Count: 109 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RC-RNASE6 RIBONUCLEASE	A	105	Aquarana catesbeiana	Mutation(s): 0
UniProt
Find proteins for Q9DFY5 (Aquarana catesbeiana) Explore Q9DFY5  Go to UniProtKB:  Q9DFY5

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(*AP*CP*GP*AP)-3'	B	4	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PCA	A	L-PEPTIDE LINKING	C5 H7 N O3		GLN

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.273 (Depositor), 0.278 (DCC) 
• R-Value Work:  0.229 (Depositor), 0.235 (DCC) 
• R-Value Observed: 0.229 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.23	α = 90
b = 61.23	β = 90
c = 65.88	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-07-15 
Deposition Author(s): Tsai, C.-J., Liu, J.-H., Liao, Y.-D., Chen, L.-Y., Cheng, P.-T., Sun, Y.-J.

Revision History  

• Version 1.0: 2004-07-15
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 2.0: 2020-03-11
  Changes: Derived calculations, Other, Polymer sequence
• Version 2.1: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 2.2: 2024-10-16
  Changes: Structure summary