PDB-9h6h: Bacteroides ovatus GH98 endoxylanase with Seleno-methionine subst...

ID or keywords:

Entry

Database: PDB / ID: 9h6h

Title

Bacteroides ovatus GH98 endoxylanase with Seleno-methionine substituents

Components

Glycosyl hydrolase family 98

Keywords

HYDROLASE / Bacteroides ovatus / GH98 / endoxylanase / SeMet

Function / homology

Function and homology information

carbohydrate binding / carbohydrate metabolic process / hydrolase activity
Similarity search - Function

Biological species

Bacteroides ovatus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2 Å

Authors

Tomlinson, C.W.E. / Cartmell, A. / Bolam, D.N.

Funding support

1items

Citation

Journal: To Be Published
Title: Seleno-Methionine substituted structure of Bacteriodes ovatus GH98
Authors: Tomlinson, C.W.E. / Cartmell, A. / Bolam, D.N.

History

Deposition	Oct 24, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Nov 5, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	9h6h.cif.gz	1.6 MB	Display	PDBx/mmCIF format
PDB format	pdb9h6h.ent.gz	1.1 MB	Display	PDB format
PDBx/mmJSON format	9h6h.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9h6h_validation.pdf.gz	463 KB	Display	wwPDB validaton report
Full document	9h6h_full_validation.pdf.gz	476.5 KB	Display
Data in XML	9h6h_validation.xml.gz	87.9 KB	Display
Data in CIF	9h6h_validation.cif.gz	121.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/h6/9h6h ftp://data.pdbj.org/pub/pdb/validation_reports/h6/9h6h	HTTPS FTP

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Related structure data

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	#156 - Dec 2012 ABO Blood Type Glycosyltransferases similarity (5)

Deposited unit

A: Glycosyl hydrolase family 98

B: Glycosyl hydrolase family 98

hetero molecules

206 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Glycosyl hydrolase family 98

hetero molecules

defined by author
Evidence: gel filtration
103 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Glycosyl hydrolase family 98

hetero molecules

defined by author
Evidence: gel filtration
103 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	183.914, 62.447, 178.713
Angle α, β, γ (deg.)	90, 118.058, 90
Int Tables number	5
Space group name H-M	C121

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: ARG / End label comp-ID: ARG / Auth seq-ID: 46 - 938 / Label seq-ID: 5 - 897

Dom-ID	Auth asym-ID	Label asym-ID
1	A	A
2	B	B

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

#1: Protein	Glycosyl hydrolase family 98 / GH98 endoxylanase Mass: 102696.641 Da / Num. of mol.: 2 / Mutation: E361A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides ovatus (bacteria) / Gene: F3F51_01075, HUV13_02585 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A6N3VET1
#2: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#3: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1261 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.21 Å³/Da / Density % sol: 44.46 %
Crystal grow	Temperature: 294 K / Method: vapor diffusion / Details: PEG based

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

Diamond

/ Beamline: I04 / Wavelength: 0.9795 Å

Detector

Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 25, 2022

Radiation

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

Radiation wavelength

Wavelength: 0.9795 Å / Relative weight: 1

Reflection

Resolution: 2→58.47 Å / Num. obs: 121030 / % possible obs: 99.8 % / Redundancy: 19.4 % / CC_1/2: 0.987 / Net I/σ(I): 5.5

Reflection shell

Resolution (Å)	Mean I/σ(I) obs	Num. unique obs	CC_1/2	Diffraction-ID
10.95-58.4	15.1	812	0.997	1
2-2.03	1.1	5917	0.397	1

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0430 (refmacat 0.4.82)	refinement
DIALS		data reduction
Aimless		data scaling
PHASER		phasing
Coot		model building

Refinement

Method to determine structure:

SAD / Resolution: 2→58.4 Å / Cor.coef. F_o:F_c: 0.948 / Cor.coef. F_o:F_c free: 0.917 / SU B: 11.961 / SU ML: 0.166 / Cross valid method: FREE R-VALUE / ESU R: 0.213 / ESU R Free: 0.182
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2418	6152	5.084 %
R_work	0.1922	114853	-
all	0.195	-	-
obs	-	121005	99.627 %

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: 29.655 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.71 Å²	-0 Å²	0.808 Å²
2-	-	-0.834 Å²	-0 Å²
3-	-	-	-0.47 Å²

Refinement step

Cycle: LAST / Resolution: 2→58.4 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14240	0	51	1261	15552

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.012	14680
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	13331
X-RAY DIFFRACTION	r_angle_refined_deg	1.594	1.794	19964
X-RAY DIFFRACTION	r_angle_other_deg	0.554	1.755	30699
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.736	5	1797
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	9.768	5	68
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.923	10	2287
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	15.428	10	720
X-RAY DIFFRACTION	r_chiral_restr	0.079	0.2	2150
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	17575
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	3553
X-RAY DIFFRACTION	r_nbd_refined	0.207	0.2	2936
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.19	0.2	12877
X-RAY DIFFRACTION	r_nbtor_refined	0.185	0.2	7323
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.085	0.2	7811
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.183	0.2	1109
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.048	0.2	1
X-RAY DIFFRACTION	r_metal_ion_refined	0.149	0.2	6
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.265	0.2	58
X-RAY DIFFRACTION	r_nbd_other	0.195	0.2	139
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.279	0.2	44
X-RAY DIFFRACTION	r_mcbond_it	1.764	1.844	7182
X-RAY DIFFRACTION	r_mcbond_other	1.764	1.844	7182
X-RAY DIFFRACTION	r_mcangle_it	2.857	3.306	8981
X-RAY DIFFRACTION	r_mcangle_other	2.857	3.306	8982
X-RAY DIFFRACTION	r_scbond_it	2.113	2.045	7498
X-RAY DIFFRACTION	r_scbond_other	2.113	2.046	7499
X-RAY DIFFRACTION	r_scangle_it	3.41	3.649	10983
X-RAY DIFFRACTION	r_scangle_other	3.41	3.649	10984
X-RAY DIFFRACTION	r_lrange_it	5.762	21.431	17089
X-RAY DIFFRACTION	r_lrange_other	5.705	20.853	16849
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.075	0.05	30502

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.07487	0.0501
1	2	B	X-RAY DIFFRACTION	Local ncs	0.07487	0.0501

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
2-2.052	0.328	439	0.302	8371	0.303	8909	0.915	0.928	98.8888	0.304
2.052-2.108	0.324	437	0.286	8209	0.287	8706	0.921	0.937	99.3108	0.285
2.108-2.169	0.303	418	0.262	7936	0.264	8401	0.935	0.948	99.4405	0.26
2.169-2.236	0.282	394	0.242	7819	0.243	8262	0.936	0.957	99.4069	0.239
2.236-2.309	0.275	426	0.228	7519	0.231	7983	0.948	0.963	99.524	0.224
2.309-2.39	0.264	412	0.214	7231	0.216	7679	0.954	0.968	99.5312	0.205
2.39-2.48	0.281	347	0.217	7085	0.22	7454	0.944	0.968	99.7049	0.206
2.48-2.581	0.26	321	0.197	6792	0.2	7132	0.954	0.974	99.7336	0.186
2.581-2.695	0.279	337	0.199	6565	0.203	6918	0.952	0.974	99.7687	0.185
2.695-2.827	0.241	320	0.189	6246	0.191	6576	0.963	0.977	99.8479	0.175
2.827-2.979	0.235	321	0.163	5950	0.167	6279	0.966	0.983	99.8726	0.151
2.979-3.159	0.234	309	0.176	5602	0.179	5911	0.963	0.981	100	0.164
3.159-3.377	0.237	294	0.172	5285	0.175	5579	0.964	0.982	100	0.161
3.377-3.646	0.227	275	0.179	4942	0.182	5217	0.967	0.98	100	0.172
3.646-3.993	0.213	267	0.165	4524	0.168	4792	0.97	0.983	99.9791	0.159
3.993-4.462	0.199	226	0.144	4165	0.147	4391	0.977	0.987	100	0.141
4.462-5.147	0.189	202	0.139	3646	0.142	3848	0.979	0.986	100	0.138
5.147-6.291	0.222	181	0.174	3109	0.176	3290	0.971	0.984	100	0.168
6.291-8.846	0.178	135	0.16	2454	0.161	2589	0.983	0.986	100	0.155
8.846-58.4	0.2	91	0.201	1403	0.201	1503	0.976	0.973	99.4012	0.243

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	0.4876	-0.1795	-0.024	0.5511	0.0203	0.2644	0.0136	-0.0226	-0.0039	-0.0213	-0.0078	-0.0461	0.0195	0.0291	-0.0058	0.1129	-0.0114	0.0198	0.0972	-0.0025	0.008	60.2072	20.6964	138.6075
2	0.5065	0.125	-0.0897	0.389	-0.0134	0.2642	0.0056	0.0191	-0.0183	0.03	-0.0067	0.014	0.0157	-0.026	0.0011	0.0816	0.0062	0.0202	0.0502	0.0015	0.0063	-0.2783	19.0056	98.4187

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	A	43 - 939
2	X-RAY DIFFRACTION	2	ALL	B	46 - 939

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