2C46 | pdb_00002c46

CRYSTAL STRUCTURE OF THE HUMAN RNA guanylyltransferase and 5'- phosphatase

• PDB DOI: https://doi.org/10.2210/pdb2C46/pdb

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


• Deposited: 2005-10-15 Released: 2005-11-01 
• Deposition Author(s): Debreczeni, J., Johansson, C., Longman, E., Gileadi, O., SavitskySmee, P., Smee, C., Bunkoczi, G., Ugochukwu, E., von Delft, F., Sundstrom, M., Weigelt, J., Arrowsmith, C., Edwards, A., Knapp, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.234 (Depositor), 0.242 (DCC) 
• R-Value Work: 
  0.204 (Depositor) 
• R-Value Observed: 
  0.206 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of the Human RNA Guanylyltransferase and 5'-Phosphatase

Debreczeni, J., Johansson, C., Longman, E., Gileadi, O., Savitskysmee, P., Smee, C., Bunkoczi, G., Ugochukwu, E., von Delft, F., Sundstrom, M., Weigelt, J., Arrowsmith, C., Edwards, A., Knapp, S.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 generated by PISA (software)

Biological Assembly 5  

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

Biological assembly 5 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 110.75 kDa 
• Atom Count: 6,719 
• Modeled Residue Count: 787 
• Deposited Residue Count: 964 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MRNA CAPPING ENZYME	A, B, C, D	241	Homo sapiens	Mutation(s): 0  EC: 2.7.7.50 (PDB Primary Data), 3.6.1.74 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for O60942 (Homo sapiens) Explore O60942  Go to UniProtKB:  O60942
PHAROS:  O60942 GTEx:  ENSG00000111880

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.234 (Depositor), 0.242 (DCC) 
• R-Value Work:  0.204 (Depositor) 
• R-Value Observed: 0.206 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.4	α = 90
b = 161.6	β = 104.7
c = 60.7	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-11-01 
Deposition Author(s): Debreczeni, J., Johansson, C., Longman, E., Gileadi, O., SavitskySmee, P., Smee, C., Bunkoczi, G., Ugochukwu, E., von Delft, F., Sundstrom, M., Weigelt, J., Arrowsmith, C., Edwards, A., Knapp, S.

Revision History  

• Version 1.0: 2005-11-01
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2012-12-05
  Changes: Database references, Structure summary
• Version 1.3: 2018-01-24
  Changes: Database references
• Version 1.4: 2023-12-13
  Changes: Data collection, Database references, Other, Refinement description