PDB-9thw: Bacteriodes thetaiotamicron sulphatase BT1636_S77C in complex wit...

ID or keywords:

Entry

Database: PDB / ID: 9thw

Title

Bacteriodes thetaiotamicron sulphatase BT1636_S77C in complex with Molybdate Ions

Components

Arylsulfatase

Keywords

SUGAR BINDING PROTEIN / Carbohydrate / Sulphatase / Complex / Inhibitor

Function / homology

Function and homology information

hydrolase activity / metal ion binding
Similarity search - Function

Biological species

Bacteroides thetaiotaomicron (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.4 Å

Authors

Tomlinson, C.W.E. / Cartmell, A.

Funding support

United Kingdom, 1items

Citation

Journal: Angew.Chem.Int.Ed.Engl. / Year: 2026
Title: Fluorogenic Coupled Assays Reveal Catalytic Properties, Inhibition Constants and Cellular Location of Mucin-Active Carbohydrate Sulfatases.
Authors: Tomlinson, C.W.E. / Bergers, M.D. / Bolam, D.N. / Luis, A.S. / Cartmell, A. / Armstrong, Z.

History

Deposition	Dec 4, 2025	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Aug 26, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9thw.cif.gz	365.2 KB	Display	PDBx/mmCIF format
PDB format	pdb9thw.ent.gz	280.1 KB	Display	PDB format
PDBx/mmJSON format	9thw.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/th/9thw ftp://data.pdbj.org/pub/pdb/validation_reports/th/9thw	HTTPS FTP

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Related structure data

Related structure data	9thuC 9thvC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#50 - Feb 2004 Glycolytic Enzymes similarity (1)

Deposited unit

A: Arylsulfatase

hetero molecules

58.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	74.7, 87.26, 103.13
Angle α, β, γ (deg.)	90, 90, 90
Int Tables number	19
Space group name H-M	P2₁2₁2₁

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Protein , 1 types, 1 molecules A

#1: Protein	Arylsulfatase Mass: 58029.316 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria) Gene: BT_1636 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8A789

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Non-polymers , 5 types, 464 molecules

#2: Chemical	ChemComp-MOO / MOLYBDATE ION / MOLYBDATE Mass: 159.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: MoO₄ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₆H₁₄O₂ / Comment: precipitant*YM
#4: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#5: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 457 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y
Has protein modification	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 3.06 Å³/Da / Density % sol: 59.78 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 40% MPD, 5% PEG 8000, 100mM Sodium Cacodylate pH 6.5

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

Diamond

/ Beamline: I04 / Wavelength: 0.7601 Å

Detector

Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Nov 21, 2025

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.7601 Å / Relative weight: 1

Reflection

Resolution: 1.4→51.56 Å / Num. obs: 132964 / % possible obs: 100 % / Redundancy: 13.7 % / CC_1/2: 0.999 / R_merge(I) obs: 0.105 / R_pim(I) all: 0.042 / R_rim(I) all: 0.114 / Χ²: 1 / Net I/σ(I): 10

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	Χ²	% possible all
7.67-51.56	11.2	0.039	49.4	10534	941	0.999	0.016	0.042	1	99.7
1.4-1.42	13.4	3.83	0.7	86861	6486	0.501	1.575	4.144	0.86	100

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0431 (refmacat 0.4.105)	refinement
Aimless		data scaling
DIMPLE		phasing
XDS		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.4→51.56 Å / Cor.coef. F_o:F_c: 0.984 / Cor.coef. F_o:F_c free: 0.979 / Cross valid method: FREE R-VALUE / ESU R: 0.042 / ESU R Free: 0.042
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.157	6597	4.965 %	RANDOM
R_work	0.1308	126273	-	-
all	0.132	-	-	-
obs	-	132870	99.995 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 24.043 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.779 Å²	0 Å²	0 Å²
2-	-	1.036 Å²	0 Å²
3-	-	-	-0.257 Å²

Refinement step

Cycle: LAST / Resolution: 1.4→51.56 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3869	0	42	457	4368

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.012	4026
X-RAY DIFFRACTION	r_bond_other_d	0	0.016	3661
X-RAY DIFFRACTION	r_angle_refined_deg	1.82	1.835	5448
X-RAY DIFFRACTION	r_angle_other_deg	0.62	1.767	8470
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.944	5	483
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	6.477	5	17
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.905	10	660
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	15.947	10	200
X-RAY DIFFRACTION	r_chiral_restr	0.098	0.2	547
X-RAY DIFFRACTION	r_gen_planes_refined	0.011	0.02	4716
X-RAY DIFFRACTION	r_gen_planes_other	0.022	0.02	940
X-RAY DIFFRACTION	r_nbd_refined	0.211	0.2	756
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.203	0.2	3500
X-RAY DIFFRACTION	r_nbtor_refined	0.186	0.2	1972
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.086	0.2	2044
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.172	0.2	369
X-RAY DIFFRACTION	r_metal_ion_refined	0.105	0.2	4
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.087	0.2	6
X-RAY DIFFRACTION	r_nbd_other	0.18	0.2	10
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.2	0.2	22
X-RAY DIFFRACTION	r_mcbond_it	5.515	2.114	1932
X-RAY DIFFRACTION	r_mcbond_other	5.51	2.114	1932
X-RAY DIFFRACTION	r_mcangle_it	7.533	3.803	2415
X-RAY DIFFRACTION	r_mcangle_other	7.557	3.805	2416
X-RAY DIFFRACTION	r_scbond_it	8.484	2.426	2094
X-RAY DIFFRACTION	r_scbond_other	8.431	2.427	2091
X-RAY DIFFRACTION	r_scangle_it	11.588	4.312	3033
X-RAY DIFFRACTION	r_scangle_other	11.486	4.31	3028
X-RAY DIFFRACTION	r_lrange_it	13.968	22.782	4676
X-RAY DIFFRACTION	r_lrange_other	13.237	21.586	4552
X-RAY DIFFRACTION	r_rigid_bond_restr	9.523	3	7687

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
1.4-1.436	0.315	486	0.313	9250	0.313	9736	0.92	0.917	100	0.312
1.436-1.476	0.298	456	0.288	9000	0.288	9456	0.926	0.93	100	0.285
1.476-1.518	0.256	450	0.244	8774	0.245	9225	0.948	0.95	99.9892	0.235
1.518-1.565	0.237	457	0.214	8516	0.215	8973	0.955	0.964	100	0.203
1.565-1.616	0.196	458	0.184	8243	0.185	8701	0.971	0.974	100	0.17
1.616-1.673	0.192	408	0.157	7998	0.159	8406	0.975	0.983	100	0.142
1.673-1.736	0.182	401	0.138	7751	0.14	8152	0.977	0.987	100	0.121
1.736-1.807	0.159	404	0.121	7400	0.123	7804	0.984	0.99	100	0.105
1.807-1.887	0.155	381	0.107	7131	0.109	7512	0.985	0.993	100	0.093
1.887-1.979	0.15	360	0.106	6865	0.108	7226	0.987	0.993	99.9862	0.095
1.979-2.086	0.145	325	0.109	6540	0.111	6865	0.988	0.994	100	0.101
2.086-2.212	0.13	330	0.101	6148	0.103	6478	0.99	0.994	100	0.094
2.212-2.365	0.137	299	0.094	5833	0.096	6132	0.989	0.995	100	0.088
2.365-2.554	0.124	282	0.095	5427	0.096	5709	0.991	0.995	100	0.09
2.554-2.797	0.139	278	0.105	5003	0.107	5281	0.989	0.993	100	0.104
2.797-3.126	0.143	218	0.118	4572	0.119	4790	0.987	0.992	100	0.12
3.126-3.607	0.15	223	0.127	4018	0.128	4241	0.986	0.991	100	0.134
3.607-4.413	0.117	186	0.107	3468	0.108	3654	0.992	0.993	100	0.121
4.413-6.218	0.166	122	0.145	2727	0.145	2849	0.988	0.991	100	0.166
6.218-51.56	0.204	73	0.19	1609	0.191	1683	0.98	0.983	99.9406	0.221

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