6IDY | pdb_00006idy

Crystal structure of Aspergillus fumigatus lipase B

• PDB DOI: https://doi.org/10.2210/pdb6IDY/pdb

• Classification: LIPID BINDING PROTEIN
• Organism(s): Aspergillus fumigatus
• Expression System: Komagataella phaffii GS115
• Mutation(s): No 
• Membrane Protein: Yes  OPM


• Deposited: 2018-09-12 Released: 2019-09-18 
• Deposition Author(s): Wang, Y.H., Lan, D.M.
• Funding Organization(s): National Natural Science Foundation of China

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 
  0.197 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.173 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.174 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Aspergillus fumigatus lipase B

Wang, Y.H., Lan, D.M.

To be published.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 140.66 kDa 
• Atom Count: 10,079 
• Modeled Residue Count: 1,260 
• Deposited Residue Count: 1,320 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
lipase aflb	A, B, C	440	Aspergillus fumigatus	Mutation(s): 0  Gene Names: CDV57_02421 Membrane Entity: Yes
UniProt
Find proteins for Q4WG73 (Aspergillus fumigatus (strain ATCC MYA-4609 / CBS 101355 / FGSC A1100 / Af293)) Explore Q4WG73  Go to UniProtKB:  Q4WG73

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	E [auth A], H [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CA	D [auth A], F [auth B], G [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free:  0.197 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.173 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.174 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 152.19	α = 90
b = 152.19	β = 90
c = 134.29	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-09-18 
Deposition Author(s): Wang, Y.H., Lan, D.M.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	31725022

Revision History  

• Version 1.0: 2019-09-18
  Type: Initial release
  
• Version 1.1: 2019-09-25
  Changes: Data collection, Derived calculations
• Version 1.2: 2023-11-22
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-10-16
  Changes: Structure summary