8UWV | pdb_00008uwv

Crystal structure of BT3984 SusD-like from Bacteroides thetaiotaomicron VPI-5482 at 1.1 A resolution (Space group P21)

PDB DOI: https://doi.org/10.2210/pdb8UWV/pdb

Classification: SUGAR BINDING PROTEIN
Organism(s): Bacteroides thetaiotaomicron VPI-5482
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2023-11-08 Released: 2023-11-22
Deposition Author(s): Sastre, D.E., Navarro, M.V.A.S., Sundberg, E.J.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.08 Å
R-Value Free:
0.139 (Depositor), 0.140 (DCC)
R-Value Work:
0.121 (Depositor), 0.130 (DCC)
R-Value Observed:
0.122 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Crystal structure of BT3984 SusD-like from Bacteroides thetaiotaomicron VPI-5482 at 1.1 A resolution (Space group P21)

Sastre, D.E., Navarro, M.V.A.S., Sundberg, E.J.

To be published.

Macromolecule Content

Total Structure Weight: 113.64 kDa
Atom Count: 9,365
Modeled Residue Count: 991
Deposited Residue Count: 1,026
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BT3984 SusD-like	A, B	513	Bacteroides thetaiotaomicron VPI-5482	Mutation(s): 0 Gene Names: BT_3984
UniProt
Find proteins for Q8A0N7 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50)) Explore Q8A0N7 Go to UniProtKB: Q8A0N7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8A0N7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.08 Å
R-Value Free: 0.139 (Depositor), 0.140 (DCC)
R-Value Work: 0.121 (Depositor), 0.130 (DCC)
R-Value Observed: 0.122 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.37	α = 90
b = 82.592	β = 98.88
c = 100.265	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2023-11-22

Deposition Author(s):

Navarro, M.V.A.S.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	1R01GM148075-01A1

Revision History (Full details and data files)

Version 1.0: 2023-11-22
Type: Initial release

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.