5XPX | pdb_00005xpx

Structure elucidation of truncated AMS3 lipase from an Antarctic Pseudomonas

• PDB DOI: https://doi.org/10.2210/pdb5XPX/pdb

• Classification: HYDROLASE
• Organism(s): Pseudomonas sp. A3(2015c)
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2017-06-05 Released: 2018-06-20 
• Deposition Author(s): Rahman, R.N.Z.R.A., Latip, W.
• Funding Organization(s): Universiti Putra Malaysia

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.77 Å
• R-Value Free: 
  0.277 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.222 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.225 (Depositor) 

Starting Model: experimental

Literature

Structure elucidation of truncated AMS3 lipase from an Antarctic Pseudomonas

Rahman, R.N.Z.R.A., Latip, W.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: native gel electrophoresis

Macromolecule Content 

• Total Structure Weight: 96.14 kDa 
• Atom Count: 6,066 
• Modeled Residue Count: 765 
• Deposited Residue Count: 858 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lipase	A, B [auth E]	429	Pseudomonas sp. A3(2015c)	Mutation(s): 0  EC: 3.1.1.3
UniProt
Find proteins for A0A0K0PTR1 (Pseudomonas sp. A3(2015c)) Explore A0A0K0PTR1  Go to UniProtKB:  A0A0K0PTR1

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.77 Å
• R-Value Free:  0.277 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.222 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.225 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.753	α = 90
b = 94.693	β = 90
c = 126.431	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data processing
HKL-3000	data scaling
REFMAC	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-06-20 
Deposition Author(s): Rahman, R.N.Z.R.A., Latip, W.

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Funding Organization	Location	Grant Number
Universiti Putra Malaysia	Malaysia	9479200

Revision History  

• Version 1.0: 2018-06-20
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description