5CH8 | pdb_00005ch8

Crystal structure of MDLA N225Q mutant form Penicillium cyclopium

• PDB DOI: https://doi.org/10.2210/pdb5CH8/pdb

• Classification: HYDROLASE
• Organism(s): Penicillium cyclopium
• Expression System: Komagataella pastoris
• Mutation(s): Yes 
• Membrane Protein: Yes  OPM


• Deposited: 2015-07-10 Released: 2016-04-20 
• Deposition Author(s): Xu, J., Xu, H., Hou, S., Liu, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.62 Å
• R-Value Free: 
  0.166 (Depositor), 0.175 (DCC) 
• R-Value Work: 
  0.135 (Depositor), 0.148 (DCC) 
• R-Value Observed: 
  0.137 (Depositor) 

Literature

Lipase-Driven Epoxidation Is A Two-Stage Synergistic Process

Tang, Q., Popowicz, G.M., Wang, X., Liu, J., Pavlidis, I.V., Wang, Y.

(2016) ChemistrySelect 4: 836-839

• DOI: https://doi.org/10.1002/slct.201600254

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 30.62 kDa 
• Atom Count: 2,350 
• Modeled Residue Count: 270 
• Deposited Residue Count: 279 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mono- and diacylglycerol lipase	A	279	Penicillium cyclopium	Mutation(s): 1  Gene Names: mdlA EC: 3.1.1 Membrane Entity: Yes
UniProt
Find proteins for P61869 (Penicillium cyclopium) Explore P61869  Go to UniProtKB:  P61869

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	I [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	B [auth A], C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.62 Å
• R-Value Free:  0.166 (Depositor), 0.175 (DCC) 
• R-Value Work:  0.135 (Depositor), 0.148 (DCC) 
• R-Value Observed: 0.137 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 33.33	α = 61.27
b = 44.52	β = 68.65
c = 44.76	γ = 78.17

Software Package:

Software Name	Purpose
Aimless	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
iMOSFLM	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-04-20 
Deposition Author(s): Xu, J., Xu, H., Hou, S., Liu, J.

Revision History  

• Version 1.0: 2016-04-20
  Type: Initial release
  
• Version 1.1: 2017-09-27
  Changes: Data collection, Database references, Derived calculations
• Version 1.2: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary