4DYH | pdb_00004dyh

Crystal structure of glycosylated Lipase from Humicola lanuginosa at 2 Angstrom resolution

• PDB DOI: https://doi.org/10.2210/pdb4DYH/pdb

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


• Deposited: 2012-02-29 Released: 2012-04-11 
• Deposition Author(s): Singh, A., Mukherjee, J., Gupta, M.N., Sinha, M., Kaur, P., Sharma, S., Singh, T.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.283 (Depositor), 0.292 (DCC) 
• R-Value Work: 
  0.213 (Depositor), 0.243 (DCC) 
• R-Value Observed: 
  0.216 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of glycosylated Lipase from Humicola lanuginosa at 2 Angstrom resolution

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

To be published.

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: 59.13 kDa 
• Atom Count: 4,639 
• 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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	C [auth A], D [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.283 (Depositor), 0.292 (DCC) 
• R-Value Work:  0.213 (Depositor), 0.243 (DCC) 
• R-Value Observed: 0.216 (Depositor) 

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 139.955	α = 90
b = 139.955	β = 90
c = 80.537	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-04-11 
Deposition Author(s): Singh, A., Mukherjee, J., Gupta, M.N., Sinha, M., Kaur, P., Sharma, S., Singh, T.P.

Revision History  

• Version 1.0: 2012-04-11
  Type: Initial release
  
• Version 1.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 1.3: 2024-10-30
  Changes: Structure summary