3Q1D | pdb_00003q1d

The B-box domain of Trim54

• PDB DOI: https://doi.org/10.2210/pdb3Q1D/pdb

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


• Deposited: 2010-12-17 Released: 2011-01-26 
• Deposition Author(s): Walker, J.R., Yermekbayeva, L., Mackenzie, F., Dong, A., Weigelt, J., Bountra, C., Edwards, A.M., Arrowsmith, C.H., Dhe-Paganon, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 
  0.253 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.185 (Depositor) 

Starting Model: experimental

Literature

The B-Box Domain of Trim54

Walker, J.R., Yermekbayeva, L., Mackenzie, F., Dong, A., Weigelt, J., Bountra, C., Edwards, A.M., Arrowsmith, C.H., Dhe-Paganon, S.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 5.52 kDa 
• Atom Count: 404 
• Modeled Residue Count: 47 
• Deposited Residue Count: 47 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tripartite motif-containing protein 54	A	47	Homo sapiens	Mutation(s): 0  Gene Names: MURF, MURF3, RNF30, TRIM54 EC: 6.3.2
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BYV2 (Homo sapiens) Explore Q9BYV2  Go to UniProtKB:  Q9BYV2
PHAROS:  Q9BYV2 GTEx:  ENSG00000138100

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	B [auth A], C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free:  0.253 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.185 (Depositor) 

Space Group: P 6₂ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.276	α = 90
b = 47.276	β = 90
c = 87.047	γ = 120

Software Package:

Software Name	Purpose
HKL-3000	data collection
PHASER	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-01-26 
Deposition Author(s): Walker, J.R., Yermekbayeva, L., Mackenzie, F., Dong, A., Weigelt, J., Bountra, C., Edwards, A.M., Arrowsmith, C.H., Dhe-Paganon, S.

Revision History  

• Version 1.0: 2011-01-26
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description