3MGM | pdb_00003mgm

Crystal structure of human NUDT16

• PDB DOI: https://doi.org/10.2210/pdb3MGM/pdb

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


• Deposited: 2010-04-07 Released: 2011-04-20 
• Deposition Author(s): Yan, J., Lu, G., Zhang, J., Qi, J., Li, Z., Gao, F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.201 (Depositor), 0.199 (DCC) 
• R-Value Work: 
  0.184 (Depositor), 0.186 (DCC) 
• R-Value Observed: 
  0.185 (Depositor) 

Starting Model: experimental

Literature

Crystal structure and the template mRNA decapping activity of human NUDT16

Lu, G., Zhang, J., Li, Z., Zhang, Q., Qi, J., Gao, F., Peng, H., Wang, T., Gao, G.F., Yan, J.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 43.97 kDa 
• Atom Count: 2,921 
• Modeled Residue Count: 328 
• Deposited Residue Count: 400 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
U8 snoRNA-decapping enzyme	A, B	200	Homo sapiens	Mutation(s): 0  Gene Names: hNUDT16, NUDT16 EC: 3.6.1 (PDB Primary Data), 3.6.1.62 (UniProt), 3.6.1.64 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q96DE0 (Homo sapiens) Explore Q96DE0  Go to UniProtKB:  Q96DE0
PHAROS:  Q96DE0 GTEx:  ENSG00000198585

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.201 (Depositor), 0.199 (DCC) 
• R-Value Work:  0.184 (Depositor), 0.186 (DCC) 
• R-Value Observed: 0.185 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.412	α = 90
b = 79.153	β = 90
c = 97.422	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
AMoRE	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-04-20 
Deposition Author(s): Yan, J., Lu, G., Zhang, J., Qi, J., Li, Z., Gao, F.

Revision History  

• Version 1.0: 2011-04-20
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Refinement description