7QRZ

Crystal structure of B30.2 PRYSPRY domain of MID2

• PDB DOI: https://doi.org/10.2210/pdb7QRZ/pdb

• Classification: LIGASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2022-01-12 Released: 2022-05-04 
• Deposition Author(s): Chaikuad, A., Zhubi, R., Knapp, S., Structural Genomics Consortium (SGC)
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.57 Å
• R-Value Free: 0.192 
• R-Value Work: 0.162 
• R-Value Observed: 0.164 

Literature

Crystal structure of B30.2 PRYSPRY domain of MID2

Chaikuad, A., Zhubi, R., Knapp, S., Structural Genomics Consortium (SGC)

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 22.19 kDa 
• Atom Count: 1,555 
• Modelled Residue Count: 171 
• Deposited Residue Count: 190 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable E3 ubiquitin-protein ligase MID2	A	190	Homo sapiens	Mutation(s): 0  Gene Names: MID2, FXY2, RNF60, TRIM1 EC: 2.3.2.27
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UJV3 (Homo sapiens) Explore Q9UJV3  Go to UniProtKB:  Q9UJV3
PHAROS:  Q9UJV3 GTEx:  ENSG00000080561

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.57 Å
• R-Value Free: 0.192 
• R-Value Work: 0.162 
• R-Value Observed: 0.164 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.921	α = 90
b = 75.084	β = 90
c = 78.19	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-05-04 
Deposition Author(s): Chaikuad, A., Zhubi, R., Knapp, S., Structural Genomics Consortium (SGC)

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2022-05-04
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Refinement description