3S6E | pdb_00003s6e

Crystal structure of a RNA binding motif protein 39 (RBM39) from Mus musculuS at 0.95 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3S6E/pdb

• Classification: RNA BINDING PROTEIN
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-05-25 Released: 2011-06-15 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG), Partnership for T-Cell Biology (TCELL)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 0.95 Å
• R-Value Free: 
  0.132 (Depositor), 0.140 (DCC) 
• R-Value Work: 
  0.119 (Depositor), 0.130 (DCC) 
• R-Value Observed: 
  0.120 (Depositor) 

Literature

Crystal structure of a RNA binding motif protein 39 (RBM39) from Mus musculus at 0.95 A resolution

Joint Center for Structural Genomics (JCSG), Partnership for T-Cell Biology (TCELL)

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)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 25.8 kDa 
• Atom Count: 2,425 
• Modeled Residue Count: 224 
• Deposited Residue Count: 228 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA-binding protein 39	A, B	114	Mus musculus	Mutation(s): 0  Gene Names: BC030493, Caper, Rbm39, Rnpc2
UniProt & NIH Common Fund Data Resources
Find proteins for Q8VH51 (Mus musculus) Explore Q8VH51  Go to UniProtKB:  Q8VH51
IMPC:  MGI:2157953

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CIT	E [auth B]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N
GOL	C [auth A], D [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 0.95 Å
• R-Value Free:  0.132 (Depositor), 0.140 (DCC) 
• R-Value Work:  0.119 (Depositor), 0.130 (DCC) 
• R-Value Observed: 0.120 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33S6E

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.701	α = 90
b = 55.139	β = 90
c = 84.601	γ = 90

Software Package:

Software Name	Purpose
MolProbity	model building
PDB_EXTRACT	data extraction
SHELX	phasing
SHARP	phasing
SCALA	data scaling
REFMAC	refinement
MOSFLM	data reduction
SHELXD	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-06-15 
Deposition Author(s): Joint Center for Structural Genomics (JCSG), Partnership for T-Cell Biology (TCELL)

Revision History  

• Version 1.0: 2011-06-15
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2011-08-10
  Changes: Database references
• Version 1.3: 2015-10-21
  Changes: Database references, Structure summary
• Version 1.4: 2017-10-25
  Changes: Author supporting evidence, Refinement description
• Version 1.5: 2023-02-01
  Changes: Database references, Derived calculations
• Version 1.6: 2024-11-20
  Changes: Data collection, Structure summary