3U1X

Crystal structure of a putative glycosyl hydrolase (BDI_1869) from Parabacteroides distasonis ATCC 8503 at 1.70 A resolution

PDB DOI: https://doi.org/10.2210/pdb3U1X/pdb

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

Deposited: 2011-09-30 Released: 2011-10-26
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.197
R-Value Work: 0.158
R-Value Observed: 0.160

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of a putative glycosyl hydrolase (BDI_1869) from Parabacteroides distasonis ATCC 8503 at 1.70 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 54.49 kDa
Atom Count: 4,076
Modelled Residue Count: 441
Deposited Residue Count: 472
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
putative glycosyl hydrolase	A, B	236	Parabacteroides distasonis ATCC 8503	Mutation(s): 0 Gene Names: BDI_1869
UniProt
Find proteins for A6LD40 (Parabacteroides distasonis (strain ATCC 8503 / DSM 20701 / CIP 104284 / JCM 5825 / NCTC 11152)) Explore A6LD40 Go to UniProtKB: A6LD40
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A6LD40
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B]	C [auth A], D [auth B]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.197
R-Value Work: 0.158
R-Value Observed: 0.160
Space Group: P 1
Diffraction Data: https://doi.org/10.18430/M33U1X

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.69	α = 92.98
b = 41.214	β = 91.64
c = 77.324	γ = 117.97

Software Package:

Software Name	Purpose
MolProbity	model building
PDB_EXTRACT	data extraction
SHELX	phasing
SHARP	phasing
XSCALE	data scaling
REFMAC	refinement
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2011-10-26

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2011-10-26
Type: Initial release
Version 1.1: 2017-11-08
Changes: Refinement description
Version 1.2: 2018-01-24
Changes: Database references
Version 1.3: 2023-02-01
Changes: Database references, Derived calculations

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 R01GM133198.