7R1K | pdb_00007r1k

Phosphorylated Bacillus pumilus Lipase A

• PDB DOI: https://doi.org/10.2210/pdb7R1K/pdb

• Classification: HYDROLASE
• Organism(s): Bacillus pumilus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 
• Membrane Protein: Yes  OPM


• Deposited: 2022-02-03 Released: 2022-05-25 
• Deposition Author(s): Lund, B.A.
• Funding Organization(s): Research Council of Norway

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.165 (Depositor), 0.161 (DCC) 
• R-Value Work: 
  0.141 (Depositor), 0.137 (DCC) 
• R-Value Observed: 
  0.142 (Depositor) 

Starting Model: experimental

Literature

Structure and Mechanism of a Cold-Adapted Bacterial Lipase

Lund, B.A., Svalberg, L., Purg, M., Chukwu, G., Widersten, M., Isaksen, G.V., Brandsdal, B.O., Aqvist, J.

(2022) Biochemistry 61: 933-942

• DOI: https://doi.org/10.1021/acs.biochem.2c00087

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: homology

Macromolecule Content 

• Total Structure Weight: 20.75 kDa 
• Atom Count: 1,516 
• Modeled Residue Count: 181 
• Deposited Residue Count: 190 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lipase	A	190	Bacillus pumilus	Mutation(s): 0  Gene Names: L5 Membrane Entity: Yes
UniProt
Find proteins for W8FKE7 (Bacillus pumilus) Explore W8FKE7  Go to UniProtKB:  W8FKE7

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DEP (Subject of Investigation/LOI)	C [auth A]	DIETHYL PHOSPHONATE C4 H11 O3 P MJUJXFBTEFXVKU-UHFFFAOYSA-N
OAA	B [auth A]	OXALOACETATE ION C4 H3 O5 KHPXUQMNIQBQEV-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.165 (Depositor), 0.161 (DCC) 
• R-Value Work:  0.141 (Depositor), 0.137 (DCC) 
• R-Value Observed: 0.142 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.396	α = 90
b = 42.843	β = 91.28
c = 62.66	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
APEX 2	data collection
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-05-25 
Deposition Author(s): Lund, B.A.

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Funding Organization	Location	Grant Number
Research Council of Norway	Norway	262695
Research Council of Norway	Norway	274858

Revision History  

• Version 1.0: 2022-05-25
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.2: 2024-10-09
  Changes: Structure summary