7SPR | pdb_00007spr

Crystal structure of SMG1 mutant (G28C/P206C/Q34P/A37P/M176V/G177A/M294R/F278N)

PDB DOI: https://doi.org/10.2210/pdb7SPR/pdb

Classification: HYDROLASE
Organism(s): Malassezia globosa CBS 7966
Expression System: Komagataella phaffii
Mutation(s): Yes

Deposited: 2021-11-03 Released: 2023-05-10
Deposition Author(s): Li, L.L., Wang, Y.H.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.79 Å
R-Value Free:
0.183 (Depositor), 0.180 (DCC)
R-Value Work:
0.157 (Depositor), 0.160 (DCC)
R-Value Observed:
0.158 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Lipase SMG1 thermostability optimizing through protein design approach

Li, L.L., Wang, Y.H.

To be published.

Macromolecule Content

Total Structure Weight: 31.32 kDa
Atom Count: 2,431
Modeled Residue Count: 277
Deposited Residue Count: 277
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LIP1, secretory lipase (Family 3)	A	277	Malassezia globosa CBS 7966	Mutation(s): 8 Gene Names: MGL_0797 EC: 3.1.1
UniProt
Find proteins for A8PUY1 (Malassezia globosa (strain ATCC MYA-4612 / CBS 7966)) Explore A8PUY1 Go to UniProtKB: A8PUY1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A8PUY1
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	2		N-Glycosylation	Interactions Focus chain B Interactions & Density Focus chain B
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.79 Å
R-Value Free: 0.183 (Depositor), 0.180 (DCC)
R-Value Work: 0.157 (Depositor), 0.160 (DCC)
R-Value Observed: 0.158 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.053	α = 90
b = 48.996	β = 90
c = 110.804	γ = 90

Software Package:

Software Name	Purpose
Coot	model building
PHENIX	refinement
PHENIX	phasing
HKL-3000	data scaling
autoPROC	data processing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2023-05-10

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2023-05-10
Type: Initial release
Version 1.1: 2023-10-25
Changes: Data collection, Refinement description
Version 1.2: 2024-11-13
Changes: Structure summary

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.