3EDG | pdb_00003edg

Crystal structure of bone morphogenetic protein 1 protease domain

• PDB DOI: https://doi.org/10.2210/pdb3EDG/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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.27 Å
• R-Value Free: 
  0.177 (Depositor), 0.176 (DCC) 
• R-Value Work: 
  0.144 (Depositor), 0.145 (DCC) 
• R-Value Observed: 
  0.146 (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: 23.28 kDa 
• Atom Count: 2,041 
• Modeled Residue Count: 195 
• Deposited Residue Count: 202 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bone morphogenetic protein 1	A	202	Homo sapiens	Mutation(s): 0  Gene Names: BMP1, PCOLC EC: 3.4.24.19
UniProt & NIH Common Fund Data Resources
Find proteins for P13497 (Homo sapiens) Explore P13497  Go to UniProtKB:  P13497
PHAROS:  P13497 GTEx:  ENSG00000168487

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
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: 1.27 Å
• R-Value Free:  0.177 (Depositor), 0.176 (DCC) 
• R-Value Work:  0.144 (Depositor), 0.145 (DCC) 
• R-Value Observed: 0.146 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.432	α = 90
b = 57.26	β = 90
c = 68.8	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