3H36

Structure of an uncharacterized domain in polyribonucleotide nucleotidyltransferase from Streptococcus mutans UA159

• PDB DOI: https://doi.org/10.2210/pdb3H36/pdb

• Classification: TRANSFERASE
• Organism(s): Streptococcus mutans
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-04-15 Released: 2009-05-12 
• Deposition Author(s): Cuff, M.E., Hatzos, C., Jedrzejczak, R., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.236 
• R-Value Work: 0.199 
• R-Value Observed: 0.201 

Literature

Structure of an uncharacterized domain in polyribonucleotide nucleotidyltransferase from Streptococcus mutans UA159

Cuff, M.E., Hatzos, C., Jedrzejczak, R., Joachimiak, A.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 10.97 kDa 
• Atom Count: 783 
• Modelled Residue Count: 78 
• Deposited Residue Count: 93 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polyribonucleotide nucleotidyltransferase	A	93	Streptococcus mutans	Mutation(s): 0  Gene Names: pnp, pnpA, SMU_155 EC: 2.7.7.8
UniProt
Find proteins for Q8DWB2 (Streptococcus mutans serotype c (strain ATCC 700610 / UA159)) Explore Q8DWB2  Go to UniProtKB:  Q8DWB2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.236 
• R-Value Work: 0.199 
• R-Value Observed: 0.201 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.312	α = 90
b = 59.312	β = 90
c = 93.09	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MLPHARE	phasing
DM	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
SHELXD	phasing
SHELXE	model building
SOLVE	phasing
RESOLVE	phasing
ARP/wARP	model building
CCP4	phasing
O	model building
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-05-12 
Deposition Author(s): Cuff, M.E., Hatzos, C., Jedrzejczak, R., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2009-05-12
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description