3EDI | pdb_00003edi

Crystal structure of tolloid-like protease 1 (TLL-1) protease domain

• PDB DOI: https://doi.org/10.2210/pdb3EDI/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-09-03 Released: 2008-09-16 
• Deposition Author(s): Mac Sweeney, A.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 
  0.182 (Depositor), 0.179 (DCC) 
• R-Value Work: 
  0.154 (Depositor), 0.153 (DCC) 
• R-Value Observed: 
  0.155 (Depositor) 

Starting Model: experimental

Literature

Structural basis for the substrate specificity of bone morphogenetic protein 1/tolloid-like metalloproteases

Mac Sweeney, A., Parrado, S.G., Vinzenz, D., Bernardi, A., Hein, A., Bodendorf, U., Erbel, P., Logel, C., Gerhartz, B.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 23.55 kDa 
• Atom Count: 1,905 
• Modeled Residue Count: 195 
• Deposited Residue Count: 201 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tolloid-like protein 1	A	201	Homo sapiens	Mutation(s): 0  Gene Names: TLL1, TLL EC: 3.4.24
UniProt & NIH Common Fund Data Resources
Find proteins for O43897 (Homo sapiens) Explore O43897  Go to UniProtKB:  O43897
PHAROS:  O43897 GTEx:  ENSG00000038295

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	E [auth A], F [auth A], G [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
DMS	H [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
ZN	C [auth A], D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACE	B [auth A]	ACETYL GROUP C2 H4 O IKHGUXGNUITLKF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free:  0.182 (Depositor), 0.179 (DCC) 
• R-Value Work:  0.154 (Depositor), 0.153 (DCC) 
• R-Value Observed: 0.155 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.281	α = 90
b = 58.923	β = 104.62
c = 47.444	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-09-16 
Deposition Author(s): Mac Sweeney, A.

Revision History  

• Version 1.0: 2008-09-16
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description