5D77 | pdb_00005d77

Structure of Mip6 RRM3 Domain

• PDB DOI: https://doi.org/10.2210/pdb5D77/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: 1.30 Å
• R-Value Free: 
  0.182 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.151 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.153 (Depositor) 

Starting Model: experimental

Literature

Structure of Mip6 RRM3 domain at 1.3

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: 9.55 kDa 
• Atom Count: 737 
• Modeled Residue Count: 82 
• Deposited Residue Count: 82 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA-binding protein MIP6	A	82	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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CIT	B [auth A]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N
NO3	C [auth A], D [auth A]	NITRATE ION N O3 NHNBFGGVMKEFGY-UHFFFAOYSA-N
NA	E [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO	A	L-PEPTIDE LINKING	C3 H7 N O3 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free:  0.182 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.151 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.153 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.31	α = 90
b = 36.31	β = 90
c = 91.816	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, Derived calculations, Refinement description
• Version 1.2: 2024-11-13
  Changes: Structure summary