1Y43 | pdb_00001y43

crystal structure of aspergilloglutamic peptidase from Aspergillus niger

• PDB DOI: https://doi.org/10.2210/pdb1Y43/pdb

• Classification: HYDROLASE
• Organism(s): Aspergillus niger var. macrosporus
• Mutation(s): No 


• Deposited: 2004-11-30 Released: 2005-12-13 
• Deposition Author(s): Sasaki, H., Nakagawa, A., Iwata, S., Muramatsu, T., Suganuma, M., Sawano, Y., Kojima, M., Kubota, K., Takahashi, K.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 
  0.226 (Depositor) 
• R-Value Work: 
  0.197 (Depositor) 
• R-Value Observed: 
  0.197 (Depositor) 

Literature

The three-dimensional structure of aspergilloglutamic peptidase from Aspergillus niger

Sasaki, H., Nakagawa, A., Muramatsu, T., Suganuma, M., Sawano, Y., Kojima, M., Kubota, K., Takahashi, K., Tanokura, M.

(2004) Proc Jpn Acad Ser B Phys Biol Sci 80: 435-438

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content

• Total Structure Weight: 22.77 kDa 
• Atom Count: 1,661 
• Modelled Residue Count: 203 
• Deposited Residue Count: 212 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aspergillopepsin II light chain	A	39	Aspergillus niger var. macrosporus	Mutation(s): 0  EC: 3.4.23.19
UniProt
Find proteins for P24665 (Aspergillus niger) Explore P24665  Go to UniProtKB:  P24665

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Aspergillopepsin II heavy chain	B	173	Aspergillus niger var. macrosporus	Mutation(s): 0  EC: 3.4.23.19
UniProt
Find proteins for P24665 (Aspergillus niger) Explore P24665  Go to UniProtKB:  P24665

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth B], E [auth B], F [auth B], G [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free:  0.226 (Depositor) 
• R-Value Work:  0.197 (Depositor) 
• R-Value Observed: 0.197 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.1	α = 90
b = 70.7	β = 90
c = 38.3	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALA	data scaling
MLPHARE	phasing
X-PLOR	refinement
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-12-13 
Deposition Author(s): Sasaki, H., Nakagawa, A., Iwata, S., Muramatsu, T., Suganuma, M., Sawano, Y., Kojima, M., Kubota, K., Takahashi, K.

Revision History  

• Version 1.0: 2005-12-13
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2013-02-27
  Changes: Database references
• Version 1.4: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary