1WVM | pdb_00001wvm

Crystal Structure of Psychrophilic Subtilisin-like Serine Protease APA1 from Antarctic Psychrotroph Pseudoaleromonas sp. AS-11, Complexed with Inhibitor Chymostatin

• PDB DOI: https://doi.org/10.2210/pdb1WVM/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Pseudoalteromonas sp. AS-11, Streptomyces hygroscopicus
• Mutation(s): No 


• Deposited: 2004-12-16 Released: 2006-03-21 
• Deposition Author(s): Dong, D., Watanabe, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.206 (Depositor), 0.205 (DCC) 
• R-Value Work: 
  0.192 (Depositor), 0.191 (DCC) 
• R-Value Observed: 
  0.192 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Psychrophilic Subtilisin-like Serine Protease from Antarctic Psychrotroph Pseudoalteromonas sp. AS-11 at 0.16 nm resolution

Dong, D., Watanabe, K.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 91.87 kDa 
• Atom Count: 6,903 
• Modeled Residue Count: 879 
• Deposited Residue Count: 890 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
alkaline serine protease	A, B	441	Pseudoalteromonas sp. AS-11	Mutation(s): 0  EC: 3.4.21
UniProt
Find proteins for Q65Z69 (Pseudoalteromonas sp. AS-11) Explore Q65Z69  Go to UniProtKB:  Q65Z69

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CHYMOSTATIN	C, D	4	Streptomyces hygroscopicus	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	E [auth A], F [auth A], J [auth B], K [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG	G [auth A], H [auth A], I [auth A], L [auth B], M [auth B], N [auth B], O [auth B], P [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PHA	C, D	L-PEPTIDE LINKING	C9 H11 N O		PHE

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000558	C, D	Chymostatin A	Oligopeptide / Enzyme inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.206 (Depositor), 0.205 (DCC) 
• R-Value Work:  0.192 (Depositor), 0.191 (DCC) 
• R-Value Observed: 0.192 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 123.23	α = 90
b = 138.34	β = 97.56
c = 64.88	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-03-21 
Deposition Author(s): Dong, D., Watanabe, K.

Revision History  

• Version 1.0: 2006-03-21
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Source and taxonomy, Structure summary, Version format compliance
• Version 1.3: 2013-02-27
  Changes: Other
• Version 2.0: 2023-10-25
  Changes: Advisory, Data collection, Database references, Derived calculations, Polymer sequence, Refinement description
• Version 2.1: 2024-10-30
  Changes: Derived calculations, Structure summary