3MD1 | pdb_00003md1

Crystal Structure of the Second RRM Domain of Yeast Poly(U)-Binding Protein (Pub1)

• PDB DOI: https://doi.org/10.2210/pdb3MD1/pdb

• Classification: RNA BINDING PROTEIN
• Organism(s): Saccharomyces cerevisiae
• Mutation(s): No 


• Deposited: 2010-03-29 Released: 2010-05-05 
• Deposition Author(s): Li, H., Shi, H., Li, Y., Cui, Y., Niu, L., Teng, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.221 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.198 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.199 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of the Second RRM Domain of Yeast Poly(U)-Binding Protein (Pub1)

Li, H., Shi, H., Li, Y., Cui, Y., Niu, L., Teng, M.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 3 generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 4 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 18.95 kDa 
• Atom Count: 1,472 
• Modeled Residue Count: 162 
• Deposited Residue Count: 166 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1	A, B	83	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P32588 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P32588  Go to UniProtKB:  P32588

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A], D [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.221 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.198 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.199 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.661	α = 90
b = 72.661	β = 90
c = 81.989	γ = 120

Software Package:

Software Name	Purpose
MAR345dtb	data collection
PHASES	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-05-05 
Deposition Author(s): Li, H., Shi, H., Li, Y., Cui, Y., Niu, L., Teng, M.

Revision History  

• Version 1.0: 2010-05-05
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description