7Z3X | pdb_00007z3x

Crystal structure of FIR RRM1-2 Y115F mutant bound to FUSE ssDNA

• PDB DOI: https://doi.org/10.2210/pdb7Z3X/pdb
• NAKB: 7Z3X

• Classification: DNA BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2022-03-02 Released: 2022-11-09 
• Deposition Author(s): Ni, X., Chaikuad, A., Knapp, S., Structural Genomics Consortium (SGC)
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.214 (Depositor), 0.214 (DCC) 
• R-Value Work: 
  0.204 (Depositor), 0.204 (DCC) 
• R-Value Observed: 
  0.204 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of FIR RRM1-2 Y115F mutant bound to FUSE ssDNA

Ni, X., Chaikuad, A., Knapp, S.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 45.62 kDa 
• Atom Count: 3,193 
• Modeled Residue Count: 394 
• Deposited Residue Count: 400 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Poly(U)-binding-splicing factor PUF60	A, B	197	Homo sapiens	Mutation(s): 1  Gene Names: PUF60, FIR, ROBPI, SIAHBP1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UHX1 (Homo sapiens) Explore Q9UHX1  Go to UniProtKB:  Q9UHX1
PHAROS:  Q9UHX1 GTEx:  ENSG00000179950

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*GP*TP*())-3')	C [auth D]	3	Homo sapiens

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*TP*T)-3')	D [auth E]	3	Homo sapiens

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	E [auth A], F [auth A], G [auth B], H [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.214 (Depositor), 0.214 (DCC) 
• R-Value Work:  0.204 (Depositor), 0.204 (DCC) 
• R-Value Observed: 0.204 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.613	α = 90
b = 70.386	β = 90
c = 107.353	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-11-09 
Deposition Author(s): Ni, X., Chaikuad, A., Knapp, S., Structural Genomics Consortium (SGC)

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2022-11-09
  Type: Initial release
  
• Version 1.1: 2022-11-23
  Changes: Derived calculations
• Version 2.0: 2023-01-11
  Type: Coordinate replacement
  Reason: Model completeness
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Refinement description, Source and taxonomy, Structure summary
• Version 2.1: 2024-02-07
  Changes: Data collection