3P1U

Crystal structure of a SusD homolog (BDI_0600) from Parabacteroides distasonis ATCC 8503 AT 2.05 A resolution

PDB DOI: https://doi.org/10.2210/pdb3P1U/pdb

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

Deposited: 2010-09-30 Released: 2010-11-03
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free: 0.265
R-Value Work: 0.243
R-Value Observed: 0.244

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of a SusD homolog (YP_001301998.1) from Parabacteroides distasonis ATCC 8503 at 2.05 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 119.57 kDa
Atom Count: 8,729
Modelled Residue Count: 1,030
Deposited Residue Count: 1,058
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SusD homolog	A, B	529	Parabacteroides distasonis ATCC 8503	Mutation(s): 0 Gene Names: BDI_0600
UniProt
Find proteins for A6L9L2 (Parabacteroides distasonis (strain ATCC 8503 / DSM 20701 / CIP 104284 / JCM 5825 / NCTC 11152)) Explore A6L9L2 Go to UniProtKB: A6L9L2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A6L9L2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain C [auth B] MOL2 format, chain C [auth B]	C [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth B] Interactions & Density Focus chain C [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: 2.05 Å
R-Value Free: 0.265
R-Value Work: 0.243
R-Value Observed: 0.244
Space Group: P 6
Diffraction Data: https://doi.org/10.18430/M33P1U

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 130.242	α = 90
b = 130.242	β = 90
c = 114.822	γ = 120

Software Package:

Software Name	Purpose
SOLVE	phasing
BUSTER-TNT	refinement
SCALA	data processing
PDB_EXTRACT	data extraction
MOSFLM	data reduction
SCALA	data scaling
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: 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.