1VCZ

Crystal structure of the RNase NT in complex with 5'-GMP

• PDB DOI: https://doi.org/10.2210/pdb1VCZ/pdb

• Classification: HYDROLASE
• Organism(s): Nicotiana glutinosa
• Expression System: Komagataella pastoris
• Mutation(s): No 


• Deposited: 2004-03-17 Released: 2005-04-26 
• Deposition Author(s): Kawano, S., Kakuta, Y., Kimura, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.252 
• R-Value Work: 0.217 
• R-Value Observed: 0.217 

Literature

Crystal Structure of the Nicotiana glutinosa Ribonuclease NT in Complex with Nucleotide Monophosphates

Kawano, S., Kakuta, Y., Kimura, M.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 25.72 kDa 
• Atom Count: 1,788 
• Modelled Residue Count: 204 
• Deposited Residue Count: 217 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RNase NGR3	A	217	Nicotiana glutinosa	Mutation(s): 0  EC: 3.1.27.1
UniProt
Find proteins for Q9SSV1 (Nicotiana glutinosa) Explore Q9SSV1  Go to UniProtKB:  Q9SSV1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
5GP	B [auth A], C [auth A]	GUANOSINE-5'-MONOPHOSPHATE C10 H14 N5 O8 P RQFCJASXJCIDSX-UUOKFMHZSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.252 
• R-Value Work: 0.217 
• R-Value Observed: 0.217 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.28	α = 90
b = 69.547	β = 90
c = 73.969	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-04-26 
Deposition Author(s): Kawano, S., Kakuta, Y., Kimura, M.

Revision History  

• Version 1.0: 2005-04-26
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description