4YUD | pdb_00004yud

Crystal structure of a RNA binding motif protein 39 (RBM39) from Homo sapiens at 1.28 A resolution

• PDB DOI: https://doi.org/10.2210/pdb4YUD/pdb

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


• Deposited: 2015-03-18 Released: 2015-04-01 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG), Partnership for T-Cell Biology (TCELL)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.28 Å
• R-Value Free: 
  0.194 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.146 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.149 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a RNA binding motif protein 39 (RBM39) from Homo sapiens at 1.28 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)

Macromolecule Content 

• Total Structure Weight: 10.3 kDa 
• Atom Count: 846 
• Modeled Residue Count: 87 
• Deposited Residue Count: 92 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA-binding protein 39	A	92	Homo sapiens	Mutation(s): 0  Gene Names: RBM39, HCC1, RNPC2
UniProt & NIH Common Fund Data Resources
Find proteins for Q14498 (Homo sapiens) Explore Q14498  Go to UniProtKB:  Q14498
PHAROS:  Q14498 GTEx:  ENSG00000131051

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.28 Å
• R-Value Free:  0.194 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.146 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.149 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.574	α = 90
b = 26.711	β = 90
c = 35.015	γ = 90

Software Package:

Software Name	Purpose
PDB_EXTRACT	data extraction
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-04-01 
Deposition Author(s): Joint Center for Structural Genomics (JCSG), Partnership for T-Cell Biology (TCELL)

Revision History  

• Version 1.0: 2015-04-01
  Type: Initial release
  
• Version 1.1: 2018-01-24
  Changes: Advisory, Database references, Derived calculations, Source and taxonomy
• Version 1.2: 2023-02-01
  Changes: Database references
• Version 1.3: 2023-10-25
  Changes: Data collection, Refinement description