9IHK | pdb_00009ihk

Crystal structure of carrageenan sulfatase Bt3731_S1_30A from human gut bacterium Bacteroides thetaiotaomicron VPI-3731

PDB DOI: https://doi.org/10.2210/pdb9IHK/pdb

Classification: HYDROLASE
Organism(s): Bacteroides thetaiotaomicron
Expression System: Escherichia coli K-12
Mutation(s): No

Deposited: 2025-02-21 Released: 2025-11-05
Deposition Author(s): Solanki, V., Parnami, J., Hehemann, J.H.
Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.249 (Depositor), 0.262 (DCC)
R-Value Work:
0.192 (Depositor), 0.219 (DCC)
R-Value Observed:
0.195 (Depositor)

Starting Model: in silico
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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 carrageenan sulfatase Bt3731_S1_30A from human gut bacterium Bacteroides thetaiotaomicron VPI-3731

Solanki, V., Parnami, J., Hehemann, J.H.

To be published.

Macromolecule Content

Total Structure Weight: 240.14 kDa
Atom Count: 16,282
Modeled Residue Count: 1,970
Deposited Residue Count: 2,088
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sulfatase_S1_30A	A [auth D], B [auth C], C [auth A], D [auth B]	522	Bacteroides thetaiotaomicron	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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 E [auth D] SDF format, chain F [auth C] SDF format, chain G [auth A] SDF format, chain H [auth B] MOL2 format, chain E [auth D] MOL2 format, chain F [auth C] MOL2 format, chain G [auth A] MOL2 format, chain H [auth B] mmCIF format, chain E [auth D] mmCIF format, chain F [auth C] mmCIF format, chain G [auth A] mmCIF format, chain H [auth B]	E [auth D], F [auth C], G [auth A], H [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth D] Focus chain F [auth C] Focus chain G [auth A] Focus chain H [auth B] Interactions & Density Focus chain E [auth D] Focus chain F [auth C] Focus chain G [auth A] Focus chain H [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.249 (Depositor), 0.262 (DCC)
R-Value Work: 0.192 (Depositor), 0.219 (DCC)
R-Value Observed: 0.195 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.97	α = 90
b = 115.928	β = 94.72
c = 177.205	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
DIALS	data reduction
PHASER	phasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2025-11-05

Deposition Author(s):

Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	--

Revision History (Full details and data files)

Version 1.0: 2025-11-05
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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.