3SEE

Crystal structure of a putative sugar binding protein (BT_4411) from Bacteroides thetaiotaomicron VPI-5482 at 1.25 A resolution

PDB DOI: https://doi.org/10.2210/pdb3SEE/pdb

Classification: SUGAR BINDING PROTEIN
Organism(s): Bacteroides thetaiotaomicron
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2011-06-10 Released: 2011-08-03
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.25 Å
R-Value Free: 0.149
R-Value Work: 0.130
R-Value Observed: 0.131

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of a Hypothetical sugar binding protein (BT_4411) from Bacteroides thetaiotaomicron VPI-5482 at 1.25 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 24.59 kDa
Atom Count: 2,318
Modelled Residue Count: 214
Deposited Residue Count: 222
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical sugar binding protein	A	222	Bacteroides thetaiotaomicron	Mutation(s): 0 Gene Names: BT_4411
UniProt
Find proteins for Q89ZG6 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50)) Explore Q89ZG6 Go to UniProtKB: Q89ZG6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q89ZG6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.25 Å
R-Value Free: 0.149
R-Value Work: 0.130
R-Value Observed: 0.131
Space Group: P 4₃ 2 2
Diffraction Data: https://doi.org/10.18430/M33SEE

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.473	α = 90
b = 50.473	β = 90
c = 228.461	γ = 90

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

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2011-08-03

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2011-08-03
Type: Initial release
Version 1.1: 2014-12-24
Changes: Structure summary
Version 1.2: 2017-11-08
Changes: Refinement description
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.