5D78 | pdb_00005d78

Structure of RRM3 Domain of Mip6 at 1.25 A Resolution

• PDB DOI: https://doi.org/10.2210/pdb5D78/pdb

• Classification: RNA BINDING PROTEIN
• Organism(s): Saccharomyces cerevisiae S288C
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-08-13 Released: 2016-08-17 
• Deposition Author(s): Mohamad, N., Bravo, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.25 Å
• R-Value Free: 
  0.177 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.137 (Depositor), 0.140 (DCC) 
• R-Value Observed: 
  0.139 (Depositor) 

Starting Model: experimental

Literature

Structure of RRM3 Domain of Mip6 at 1.25 A Resolution

Mohamad, N., Bravo, J.

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: 9.36 kDa 
• Atom Count: 752 
• Modeled Residue Count: 81 
• Deposited Residue Count: 81 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA-binding protein MIP6	A	81	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: MIP6, YHR015W
UniProt
Find proteins for P38760 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P38760  Go to UniProtKB:  P38760

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
BME	B [auth A], C [auth A]	BETA-MERCAPTOETHANOL C2 H6 O S DGVVWUTYPXICAM-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
OCY	A	L-PEPTIDE LINKING	C5 H11 N O3 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.25 Å
• R-Value Free:  0.177 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.137 (Depositor), 0.140 (DCC) 
• R-Value Observed: 0.139 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 25.842	α = 90
b = 47.023	β = 109.79
c = 30.563	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-08-17 
Deposition Author(s): Mohamad, N., Bravo, J.

Revision History  

• Version 1.0: 2016-08-17
  Type: Initial release
  
• Version 1.1: 2024-01-10
  Changes: Data collection, Database references, Refinement description