3VYV | pdb_00003vyv

Crystal structure of subtilisin NAT at 1.36

• PDB DOI: https://doi.org/10.2210/pdb3VYV/pdb

• Classification: HYDROLASE
• Organism(s): Bacillus subtilis subsp. natto
• Mutation(s): No 


• Deposited: 2012-10-03 Released: 2013-10-09 
• Deposition Author(s): Ushijima, H., Fuchita, N., Kajiwara, T., Motoshima, H., Ueno, G., Watanabe, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.36 Å
• R-Value Free: 
  0.176 (Depositor), 0.187 (DCC) 
• R-Value Work: 
  0.146 (Depositor), 0.155 (DCC) 
• R-Value Observed: 
  0.148 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of subtilisin NAT at 1.36

Watanabe, K.

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)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 56.14 kDa 
• Atom Count: 4,350 
• Modeled Residue Count: 550 
• Deposited Residue Count: 550 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Subtilisin NAT	A, B	275	Bacillus subtilis subsp. natto	Mutation(s): 0  EC: 3.4.21.62
UniProt
Find proteins for P35835 (Bacillus subtilis subsp. natto) Explore P35835  Go to UniProtKB:  P35835

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A], D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA	E [auth A], F [auth A], G [auth B], H [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEB	A, B	L-PEPTIDE LINKING	C10 H13 N O5 S		SER

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.36 Å
• R-Value Free:  0.176 (Depositor), 0.187 (DCC) 
• R-Value Work:  0.146 (Depositor), 0.155 (DCC) 
• R-Value Observed: 0.148 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.682	α = 90
b = 80.039	β = 90
c = 87.449	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
MOLREP	phasing
REFMAC	refinement
d*TREK	data reduction
CrystalClear	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-10-09 
Deposition Author(s): Ushijima, H., Fuchita, N., Kajiwara, T., Motoshima, H., Ueno, G., Watanabe, K.

Revision History  

• Version 1.0: 2013-10-09
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description