2Z8X | pdb_00002z8x

Crystal structure of extracellular lipase from Pseudomonas sp. MIS38

• PDB DOI: https://doi.org/10.2210/pdb2Z8X/pdb

• Classification: HYDROLASE
• Organism(s): Pseudomonas sp. MIS38
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-09-11 Released: 2007-10-30 
• Deposition Author(s): Angkawidjaja, C., You, D.J., Matsumura, H., Koga, Y., Takano, K., Kanaya, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.48 Å
• R-Value Free: 
  0.194 (Depositor), 0.193 (DCC) 
• R-Value Work: 
  0.176 (Depositor), 0.174 (DCC) 
• R-Value Observed: 
  0.177 (Depositor) 

Literature

Crystal structure of a family I.3 lipase from Pseudomonas sp. MIS38 in a closed conformation

Angkawidjaja, C., You, D.J., Matsumura, H., Kuwahara, K., Koga, Y., Takano, K., Kanaya, S.

(2007) FEBS Lett 581: 5060-5064

• PubMed: 17923123 
• DOI: https://doi.org/10.1016/j.febslet.2007.09.048
• Primary Citation Related Structures: 
  2Z8X, 2Z8Z


• PubMed Abstract: 
  

  The crystal structure of a family I.3 lipase from Pseudomonas sp. MIS38 in a closed conformation was determined at 1.5A resolution. This structure highly resembles that of Serratia marcescens LipA in an open conformation, except for the structures of two lids. Lid1 is anchored by a Ca2+ ion (Ca1) in an open conformation, but lacks this Ca1 site and greatly changes its structure and position in a closed conformation. Lid2 forms a helical hairpin in an open conformation, but does not form it and covers the active site in a closed conformation. Based on these results, we discuss on the lid-opening mechanism.

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Organizational Affiliation: 
• Department of Material and Life Science, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan.

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: 65.1 kDa 
• Atom Count: 5,334 
• Modeled Residue Count: 616 
• Deposited Residue Count: 617 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lipase	A	617	Pseudomonas sp. MIS38	Mutation(s): 0  EC: 3.1.1.3
UniProt
Find proteins for Q9RBY1 (Pseudomonas sp. MIS38) Explore Q9RBY1  Go to UniProtKB:  Q9RBY1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	L [auth A], M [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.48 Å
• R-Value Free:  0.194 (Depositor), 0.193 (DCC) 
• R-Value Work:  0.176 (Depositor), 0.174 (DCC) 
• R-Value Observed: 0.177 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.972	α = 90
b = 84.3	β = 96.32
c = 86.849	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SHELXS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-10-30 
Deposition Author(s): Angkawidjaja, C., You, D.J., Matsumura, H., Koga, Y., Takano, K., Kanaya, S.

Revision History  

• Version 1.0: 2007-10-30
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-03-13
  Changes: Data collection, Database references, Derived calculations