2VKQ | pdb_00002vkq

Crystal structure of human cytosolic 5'-nucleotidase III (cN-III, NT5C3) in complex with beryllium trifluoride

• PDB DOI: https://doi.org/10.2210/pdb2VKQ/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2007-12-21 Released: 2008-01-08 
• Deposition Author(s): Wallden, K., Moche, M., Arrowsmith, C.H., Berglund, H., Busam, R., Collins, R., Dahlgren, L.G., Edwards, A., Flodin, S., Flores, A., Graslund, S., Hammarstrom, M., Herman, M.D., Johansson, A., Johansson, I., Kallas, A., Karlberg, T., Kotenyova, T., Lehtio, L., Nilsson, M.E., Nyman, T., Persson, C., Sagemark, J., Thorsell, A.G., Tresaugues, L., van den Berg, S., Weigelt, J., Welin, M., Nordlund, P., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.242 (Depositor), 0.238 (DCC) 
• R-Value Work: 
  0.210 (Depositor), 0.209 (DCC) 
• R-Value Observed: 
  0.211 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Human Cytosolic 5'- Nucleotidase III

Wallden, K., Stenmark, P., Flodin, S., Nyman, T., Moche, M., Ehn, M., Hammarstrom, M., Nilsson-Ehle, P., Nordlund, P.

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: 33.29 kDa 
• Atom Count: 2,229 
• Modeled Residue Count: 273 
• Deposited Residue Count: 292 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CYTOSOLIC 5'-NUCLEOTIDASE III	A	292	Homo sapiens	Mutation(s): 0  EC: 3.1.3.5 (PDB Primary Data), 3.1.3.91 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H0P0 (Homo sapiens) Explore Q9H0P0  Go to UniProtKB:  Q9H0P0
PHAROS:  Q9H0P0 GTEx:  ENSG00000122643

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BEF	B [auth A]	BERYLLIUM TRIFLUORIDE ION Be F3 OGIAHMCCNXDTIE-UHFFFAOYSA-K
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.242 (Depositor), 0.238 (DCC) 
• R-Value Work:  0.210 (Depositor), 0.209 (DCC) 
• R-Value Observed: 0.211 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.265	α = 90
b = 99.388	β = 90
c = 78.041	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-01-08 
Deposition Author(s): Wallden, K., Moche, M., Arrowsmith, C.H., Berglund, H., Busam, R., Collins, R., Dahlgren, L.G., Edwards, A., Flodin, S., Flores, A., Graslund, S., Hammarstrom, M., Herman, M.D., Johansson, A., Johansson, I., Kallas, A., Karlberg, T., Kotenyova, T., Lehtio, L., Nilsson, M.E., Nyman, T., Persson, C., Sagemark, J., Thorsell, A.G., Tresaugues, L., van den Berg, S., Weigelt, J., Welin, M., Nordlund, P., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2008-01-08
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2015-04-22
  Changes: Source and taxonomy, Structure summary
• Version 1.3: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description