3GG6 | pdb_00003gg6

Crystal structure of the NUDIX domain of human NUDT18

• PDB DOI: https://doi.org/10.2210/pdb3GG6/pdb

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


• Deposited: 2009-02-27 Released: 2009-03-10 
• Deposition Author(s): Tresaugues, L., Siponen, M.I., Lehtio, L., Arrowsmith, C.H., Berglund, H., Bountra, C., Collins, R., Dahlgren, L.G., Edwards, A.M., Flodin, S., Flores, A., Graslund, S., Hammarstrom, M., Johansson, A., Johansson, I., Karlberg, T., Kotenyova, T., Moche, M., Nilsson, M.E., Nyman, T., Persson, C., Sagemark, J., Schueler, H., Thorsell, A.G., Van Den Berg, S., Weigelt, J., Welin, M., Wisniewska, M., Nordlund, P., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.226 (Depositor), 0.222 (DCC) 
• R-Value Work: 
  0.164 (Depositor), 0.159 (DCC) 
• R-Value Observed: 
  0.170 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the NUDIX domain of human NUDT18

Tresaugues, L., Siponen, M.I., Lehtio, L., Arrowsmith, C.H., Berglund, H., Bountra, C., Collins, R., Dahlgren, L.G., Edwards, A.M., Flodin, S., Flores, A., Graslund, S., Hammarstrom, M., Johansson, A., Johansson, I., Karlberg, T., Kotenyova, T., Moche, M., Nilsson, M.E., Nyman, T., Persson, C., Sagemark, J., Schueler, H., Thorsell, A.G., Van Den Berg, S., Weigelt, J., Welin, M., Wisniewska, M., 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 PISA (software)

Macromolecule Content 

• Total Structure Weight: 17.5 kDa 
• Atom Count: 1,301 
• Modeled Residue Count: 144 
• Deposited Residue Count: 156 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleoside diphosphate-linked moiety X motif 18	A	156	Homo sapiens	Mutation(s): 0  Gene Names: NUDT18 EC: 3.6.1 (PDB Primary Data), 3.6.1.76 (UniProt), 3.6.1.58 (UniProt), 3.6.1.68 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q6ZVK8 (Homo sapiens) Explore Q6ZVK8  Go to UniProtKB:  Q6ZVK8
PHAROS:  Q6ZVK8 GTEx:  ENSG00000275074

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.226 (Depositor), 0.222 (DCC) 
• R-Value Work:  0.164 (Depositor), 0.159 (DCC) 
• R-Value Observed: 0.170 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 31.66	α = 90
b = 60.13	β = 90
c = 76.09	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
PHASER	phasing
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-03-10 
Deposition Author(s): Tresaugues, L., Siponen, M.I., Lehtio, L., Arrowsmith, C.H., Berglund, H., Bountra, C., Collins, R., Dahlgren, L.G., Edwards, A.M., Flodin, S., Flores, A., Graslund, S., Hammarstrom, M., Johansson, A., Johansson, I., Karlberg, T., Kotenyova, T., Moche, M., Nilsson, M.E., Nyman, T., Persson, C., Sagemark, J., Schueler, H., Thorsell, A.G., Van Den Berg, S., Weigelt, J., Welin, M., Wisniewska, M., Nordlund, P., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2009-03-10
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-09-06
  Changes: Data collection, Database references, Refinement description