4JXM | pdb_00004jxm

Crystal structure of RRP9 WD40 repeats

• PDB DOI: https://doi.org/10.2210/pdb4JXM/pdb

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


• Deposited: 2013-03-28 Released: 2013-04-17 
• Deposition Author(s): Wu, X., Tempel, W., Xu, C., El Bakkouri, M., He, H., Seitova, A., Li, Y., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Min, J., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.92 Å
• R-Value Free: 
  0.204 (Depositor), 0.215 (DCC) 
• R-Value Work: 
  0.165 (Depositor), 0.177 (DCC) 
• R-Value Observed: 
  0.167 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of RRP9 WD40 repeats

Wu, X., Tempel, W., Xu, C., El Bakkouri, M., He, H., Seitova, A., Li, Y., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Min, J., Structural Genomics Consortium (SGC)

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 41.01 kDa 
• Atom Count: 2,752 
• Modeled Residue Count: 330 
• Deposited Residue Count: 371 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
U3 small nucleolar RNA-interacting protein 2	A	371	Homo sapiens	Mutation(s): 0  Gene Names: RRP9, RNU3IP2, U355K
UniProt & NIH Common Fund Data Resources
Find proteins for O43818 (Homo sapiens) Explore O43818  Go to UniProtKB:  O43818
PHAROS:  O43818 GTEx:  ENSG00000114767

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UNX	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A]	UNKNOWN ATOM OR ION X

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.92 Å
• R-Value Free:  0.204 (Depositor), 0.215 (DCC) 
• R-Value Work:  0.165 (Depositor), 0.177 (DCC) 
• R-Value Observed: 0.167 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.746	α = 90
b = 63.746	β = 90
c = 167.601	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
JBluIce-EPICS	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-04-17 
Deposition Author(s): Wu, X., Tempel, W., Xu, C., El Bakkouri, M., He, H., Seitova, A., Li, Y., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Min, J., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2013-04-17
  Type: Initial release
  
• Version 1.1: 2017-05-10
  Changes: Database references, Structure summary
• Version 1.2: 2017-11-15
  Changes: Refinement description
• Version 1.3: 2023-09-20
  Changes: Data collection, Database references, Refinement description