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), 0.145 (DCC)
R-Value Work:
0.121 (Depositor), 0.129 (DCC)
R-Value Observed:
0.122 (Depositor)

Starting Model: experimental
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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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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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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), 0.145 (DCC)
R-Value Work: 0.121 (Depositor), 0.129 (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

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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

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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.