1VD3 | pdb_00001vd3

Ribonuclease NT in complex with 2'-UMP

• PDB DOI: https://doi.org/10.2210/pdb1VD3/pdb

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


• Deposited: 2004-03-18 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: 
  0.251 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.209 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.209 (Depositor) 

Starting Model: experimental

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: 25.32 kDa 
• Atom Count: 1,764 
• Modeled 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
U2P	B [auth A]	PHOSPHORIC ACID MONO-[2-(2,4-DIOXO-3,4-DIHYDRO-2H-PYRIMIDIN-1-YL)-4-HYDROXY-5-HYDROXYMETHYL-TETRAHYDRO-FURAN-3-YL] ESTER C9 H13 N2 O9 P HQIDPEYTETUCNF-XVFCMESISA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.251 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.209 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.209 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.232	α = 90
b = 68.984	β = 90
c = 73.863	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
• Version 1.4: 2024-10-30
  Changes: Structure summary