3P94

Crystal structure of a GDSL-like Lipase (BDI_0976) from Parabacteroides distasonis ATCC 8503 at 1.93 A resolution

PDB DOI: https://doi.org/10.2210/pdb3P94/pdb

Classification: HYDROLASE
Organism(s): Parabacteroides distasonis ATCC 8503
Expression System: Escherichia coli
Mutation(s): No
Membrane Protein: Yes OPM

Deposited: 2010-10-15 Released: 2010-11-03
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.93 Å
R-Value Free: 0.207
R-Value Work: 0.183
R-Value Observed: 0.184

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Crystal structure of a GDSL-like Lipase (BDI_0976) from Parabacteroides distasonis ATCC 8503 at 1.93 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 92.92 kDa
Atom Count: 7,249
Modelled Residue Count: 809
Deposited Residue Count: 816
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GDSL-like Lipase	A, B, C, D	204	Parabacteroides distasonis ATCC 8503	Mutation(s): 0 Gene Names: BDI_0976 Membrane Entity: Yes
UniProt
Find proteins for A6LAN0 (Parabacteroides distasonis (strain ATCC 8503 / DSM 20701 / CIP 104284 / JCM 5825 / NCTC 11152)) Explore A6LAN0 Go to UniProtKB: A6LAN0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A6LAN0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PG4 Query on PG4 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B]	E [auth A], F [auth B]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.93 Å
R-Value Free: 0.207
R-Value Work: 0.183
R-Value Observed: 0.184
Space Group: P 1 2₁ 1
Diffraction Data: https://doi.org/10.18430/M33P94

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.8	α = 90
b = 58.36	β = 98.12
c = 98.61	γ = 90

Software Package:

Software Name	Purpose
SHELX	phasing
BUSTER-TNT	refinement
XSCALE	data processing
PDB_EXTRACT	data extraction
XDS	data reduction
XSCALE	data scaling
SHELXD	phasing
autoSHARP	phasing
BUSTER	refinement

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2010-11-03

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2010-11-03
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2011-07-20
Changes: Structure summary
Version 1.3: 2017-10-25
Changes: Author supporting evidence
Version 1.4: 2023-02-01
Changes: Database references, Derived calculations

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.