2DSN

Crystal structure of T1 lipase

• PDB DOI: https://doi.org/10.2210/pdb2DSN/pdb

• Classification: HYDROLASE
• Organism(s): Geobacillus zalihae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2006-07-03 Released: 2007-07-17 
• Deposition Author(s): Matsumura, H., Kai, Y.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.188 
• R-Value Work: 0.174 
• R-Value Observed: 0.174 

Literature

Novel cation-pi interaction revealed by crystal structure of thermoalkalophilic lipase

Matsumura, H., Yamamoto, T., Leow, T.C., Mori, T., Salleh, A.B., Basri, M., Inoue, T., Kai, Y., Rahman, R.N.Z.R.A.

(2007) Proteins 70: 592-598

• PubMed: 17932933 
• DOI: https://doi.org/10.1002/prot.21799
• Primary Citation of Related Structures:  
  2DSN, 2Z5G

---

Organizational Affiliation: 

Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1, Yamadaoka, Suita, Osaka 565-0871, Japan. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 86.71 kDa 
• Atom Count: 7,262 
• Modelled Residue Count: 774 
• Deposited Residue Count: 774 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thermostable lipase	A, B	387	Geobacillus zalihae	Mutation(s): 0  EC: 3.1.1.3
UniProt
Find proteins for Q842J9 (Geobacillus zalihae) Explore Q842J9  Go to UniProtKB:  Q842J9

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	C [auth A], G [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA	D [auth A], H [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	F [auth A], J [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	E [auth A], I [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.188 
• R-Value Work: 0.174 
• R-Value Observed: 0.174 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.731	α = 90
b = 81.27	β = 97.09
c = 99.912	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-07-17 
Deposition Author(s): Matsumura, H., Kai, Y.

Revision History  

• Version 1.0: 2007-07-17
  Type: Initial release
  
• Version 1.1: 2007-12-17
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description