3ZPX | pdb_00003zpx

USTILAGO MAYDIS LIPASE UM03410, SHORT FORM WITHOUT FLAP

• PDB DOI: https://doi.org/10.2210/pdb3ZPX/pdb

• Classification: HYDROLASE
• Organism(s): Mycosarcoma maydis
• Expression System: Komagataella pastoris
• Mutation(s): No 
• Membrane Protein: Yes  OPM


• Deposited: 2013-03-04 Released: 2014-03-19 
• Deposition Author(s): Palm, G.J., Hinrichs, W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.99 Å
• R-Value Free: 
  0.235 (Depositor), 0.234 (DCC) 
• R-Value Work: 
  0.183 (Depositor), 0.184 (DCC) 
• R-Value Observed: 
  0.185 (Depositor) 

Starting Model: experimental

Literature

Lipase from Ustilago

Brundiek, H., Palm, G.J., Bornscheuer, U.T., Hinrichs, W.

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: 99.2 kDa 
• Atom Count: 6,314 
• Modeled Residue Count: 766 
• Deposited Residue Count: 916 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LIPASE	A, B	458	Mycosarcoma maydis	Mutation(s): 0  EC: 3.1.1.3 Membrane Entity: Yes
UniProt
Find proteins for A0A0D1DXG7 (Mycosarcoma maydis) Explore A0A0D1DXG7  Go to UniProtKB:  A0A0D1DXG7

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PG4	F [auth B]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
PEG	C [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO	D [auth A], E [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.99 Å
• R-Value Free:  0.235 (Depositor), 0.234 (DCC) 
• R-Value Work:  0.183 (Depositor), 0.184 (DCC) 
• R-Value Observed: 0.185 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.753	α = 90
b = 100.15	β = 90
c = 129.158	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-03-19 
Deposition Author(s): Palm, G.J., Hinrichs, W.

Revision History  

• Version 1.0: 2014-03-19
  Type: Initial release
  
• Version 1.1: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description
• Version 1.2: 2024-11-20
  Changes: Structure summary