3P1U | pdb_00003p1u

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 (Depositor), 0.298 (DCC)
R-Value Work:
0.243 (Depositor), 0.272 (DCC)
R-Value Observed:
0.244 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3P1U

This is version 1.4 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
Modeled Residue Count: 1,030
Deposited Residue Count: 1,058
Unique protein chains: 1

Macromolecules

Find similar proteins by:

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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] mmCIF 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 (Depositor), 0.298 (DCC)
R-Value Work: 0.243 (Depositor), 0.272 (DCC)
R-Value Observed: 0.244 (Depositor)

Diffraction Data:

Space Group: P 6

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

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View more in-depth experimental data

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
Version 1.4: 2024-10-30
Changes: Data collection, 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.