4FLF | pdb_00004flf

Structure of three phase partition treated lipase from Thermomyces lanuginosa at 2.15A resolution.

• PDB DOI: https://doi.org/10.2210/pdb4FLF/pdb

• Classification: HYDROLASE
• Organism(s): Thermomyces lanuginosus
• Mutation(s): No 


• Deposited: 2012-06-14 Released: 2012-07-11 
• Deposition Author(s): Kumar, M., Mukherjee, J., Sinha, M., Kaur, P., Gupta, M.N., Sharma, S., Singh, T.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 
  0.268 (Depositor), 0.275 (DCC) 
• R-Value Work: 
  0.224 (Depositor), 0.234 (DCC) 
• R-Value Observed: 
  0.227 (Depositor) 

Starting Model: experimental

Literature

Enhancement of stability of a lipase by subjecting to three phase partitioning (TPP): structures of native and TPP-treated lipase from Thermomyces lanuginosa

Kumar, M., Mukherjee, J., Sinha, M., Kaur, P., Sharma, S., Gupta, M.N., Singh, T.P.

(2015) Sustain Chem Process 

• DOI: https://doi.org/10.1186/s40508-015-0042-5

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 59.89 kDa 
• Atom Count: 4,509 
• Modeled Residue Count: 538 
• Deposited Residue Count: 538 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lipase	A, B	269	Thermomyces lanuginosus	Mutation(s): 0  EC: 3.1.1.3
UniProt
Find proteins for O59952 (Thermomyces lanuginosus) Explore O59952  Go to UniProtKB:  O59952
Glycosylation
Glycosylation Sites: 1

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	C [auth A], J [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
XXH	I [auth A]	4-nitrobenzaldehyde C7 H5 N O3 BXRFQSNOROATLV-UHFFFAOYSA-N
GOL	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], K [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	L [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free:  0.268 (Depositor), 0.275 (DCC) 
• R-Value Work:  0.224 (Depositor), 0.234 (DCC) 
• R-Value Observed: 0.227 (Depositor) 

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 139.996	α = 90
b = 139.996	β = 90
c = 80.503	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-07-11 
Deposition Author(s): Kumar, M., Mukherjee, J., Sinha, M., Kaur, P., Gupta, M.N., Sharma, S., Singh, T.P.

Revision History  

• Version 1.0: 2012-07-11
  Type: Initial release
  
• Version 1.1: 2016-08-03
  Changes: Database references
• Version 1.2: 2020-06-24
  Changes: Advisory, Data collection, Derived calculations
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.4: 2023-11-08
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 1.5: 2024-11-20
  Changes: Structure summary