7QRY

Crystal structure of B30.2 PRYSPRY domain of MID1

• PDB DOI: https://doi.org/10.2210/pdb7QRY/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., Knapp, S., Structural Genomics Consortium (SGC)
• Funding Organization(s): Not funded

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.07 Å
• R-Value Free: 0.273 
• R-Value Work: 0.227 
• R-Value Observed: 0.229 

Starting Model: experimental

Literature

Crystal structure of B30.2 PRYSPRY domain of MID1

Chaikuad, A., 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.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Macromolecule Content

• Total Structure Weight: 84.86 kDa 
• Atom Count: 5,376 
• Modelled Residue Count: 660 
• Deposited Residue Count: 752 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase Midline-1	A, B, C, D	188	Homo sapiens	Mutation(s): 0  Gene Names: MID1, FXY, RNF59, TRIM18, XPRF EC: 2.3.2.27
UniProt & NIH Common Fund Data Resources
Find proteins for O15344 (Homo sapiens) Explore O15344  Go to UniProtKB:  O15344
PHAROS:  O15344 GTEx:  ENSG00000101871

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.07 Å
• R-Value Free: 0.273 
• R-Value Work: 0.227 
• R-Value Observed: 0.229 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.863	α = 103.76
b = 51.763	β = 92.64
c = 80.38	γ = 94.33

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., Knapp, S., Structural Genomics Consortium (SGC)

---

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