5XK2 | pdb_00005xk2

Crystal structure of mono- and diacylglycerol lipase from Aspergillus oryzae

PDB DOI: https://doi.org/10.2210/pdb5XK2/pdb

Classification: HYDROLASE
Organism(s): Aspergillus oryzae
Expression System: Escherichia coli-Pichia pastoris shuttle vector pPpARG4
Mutation(s): No
Membrane Protein: Yes OPM

Deposited: 2017-05-05 Released: 2018-05-09
Deposition Author(s): Wang, Y.H., Lan, D.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.168 (Depositor), 0.170 (DCC)
R-Value Work:
0.141 (Depositor), 0.143 (DCC)
R-Value Observed:
0.142 (Depositor)

wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of mono- and diacylglycerol lipase from Aspergillus oryzae

Wang, Y.H., Lan, D.M.

To be published.

Macromolecule Content

Total Structure Weight: 62.77 kDa
Atom Count: 4,726
Modeled Residue Count: 540
Deposited Residue Count: 572
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Diacylglycerol lipase	A, B	286	Aspergillus oryzae	Mutation(s): 0 Gene Names: mdlB, OAory_01019780 EC: 3.1.1.73 Membrane Entity: Yes
UniProt
Find proteins for P78583 (Aspergillus oryzae) Explore P78583 Go to UniProtKB: P78583
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P78583
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.168 (Depositor), 0.170 (DCC)
R-Value Work: 0.141 (Depositor), 0.143 (DCC)
R-Value Observed: 0.142 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.329	α = 90
b = 67.277	β = 95.21
c = 89.574	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2018-05-09

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2018-05-09
Type: Initial release
Version 1.1: 2024-10-30
Changes: Data collection, Database references, Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.