PDB-9euz: Glycoside hydrolase family 191 enzyme from Thermotoga maritima

ID or keywords:

Entry

Database: PDB / ID: 9euz

Title

Glycoside hydrolase family 191 enzyme from Thermotoga maritima

Components

Uncharacterized protein TM_1410

Keywords

HYDROLASE / glycoside hydrolase / Galactosamine

Function / homology

Extracellular protein / Hypothetical protein TM1410-related / Glycoside-hydrolase family GH114, TIM-barrel domain / Glycoside-hydrolase family GH114 / Aldolase-type TIM barrel / Glycoside hydrolase superfamily / Uncharacterized protein TM_1410

Function and homology information

Biological species

Thermotoga maritima MSB8 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.6 Å

Authors

Roth, C.

Funding support

Germany, 1items

Citation

Journal: To Be Published
Title: Glycoside hydrolase family 191 enzyme from Thermotoga maritima
Authors: Roth, C. / Moroz, O.V. / Miranda, S.A.D. / Jahn, L. / Blagova, E. / Lebedev, A.A. / Segura, D.R. / Stringer, M.A. / Friis, E.P. / Davies, G.J. / Wilson, K.S.

History

Deposition	Mar 28, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Apr 9, 2025	Provider: repository / Type: Initial release
Revision 1.1	Apr 23, 2025	Group: Database references / Structure summary / Category: citation / struct / Item: _citation.title / _struct.title

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9euz.cif.gz	671.4 KB	Display	PDBx/mmCIF format
PDB format	pdb9euz.ent.gz	549 KB	Display	PDB format
PDBx/mmJSON format	9euz.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/eu/9euz ftp://data.pdbj.org/pub/pdb/validation_reports/eu/9euz	HTTPS FTP

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Related structure data

Related structure data	2aam
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Uncharacterized protein TM_1410

B: Uncharacterized protein TM_1410

C: Uncharacterized protein TM_1410

D: Uncharacterized protein TM_1410

E: Uncharacterized protein TM_1410

F: Uncharacterized protein TM_1410

209 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Uncharacterized protein TM_1410

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

2

B: Uncharacterized protein TM_1410

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

3

C: Uncharacterized protein TM_1410

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

4

D: Uncharacterized protein TM_1410

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

5

E: Uncharacterized protein TM_1410

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

6

F: Uncharacterized protein TM_1410

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

Unit cell

Length a, b, c (Å)	196.055, 84.499, 196.634
Angle α, β, γ (deg.)	90, 119.828, 90
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Auth asym-ID: A / Label asym-ID: A

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth seq-ID	Label seq-ID
1	1	1	GLY	GLY	PRO	PRO	29 - 310	3 - 284
2	1	1	GLY	GLY	PRO	PRO	29 - 310	3 - 284
3	2	2	GLY	GLY	ILE	ILE	29 - 308	3 - 282
4	2	2	GLY	GLY	ILE	ILE	29 - 308	3 - 282
5	3	3	GLY	GLY	PRO	PRO	29 - 310	3 - 284
6	3	3	GLY	GLY	PRO	PRO	29 - 310	3 - 284
7	4	4	TRP	TRP	PRO	PRO	30 - 310	4 - 284
8	4	4	TRP	TRP	PRO	PRO	30 - 310	4 - 284
9	5	5	GLY	GLY	PRO	PRO	29 - 310	3 - 284
10	5	5	GLY	GLY	PRO	PRO	29 - 310	3 - 284
11	6	6	GLY	GLY	ILE	ILE	29 - 308	3 - 282
12	6	6	GLY	GLY	ILE	ILE	29 - 308	3 - 282
13	7	7	GLY	GLY	PRO	PRO	29 - 311	3 - 285
14	7	7	GLY	GLY	PRO	PRO	29 - 311	3 - 285
15	8	8	TRP	TRP	PRO	PRO	30 - 310	4 - 284
16	8	8	TRP	TRP	PRO	PRO	30 - 310	4 - 284
17	9	9	GLY	GLY	PRO	PRO	29 - 311	3 - 285
18	9	9	GLY	GLY	PRO	PRO	29 - 311	3 - 285
19	10	10	GLY	GLY	ILE	ILE	29 - 308	3 - 282
20	10	10	GLY	GLY	ILE	ILE	29 - 308	3 - 282
21	11	11	TRP	TRP	ILE	ILE	30 - 308	4 - 282
22	11	11	TRP	TRP	ILE	ILE	30 - 308	4 - 282
23	12	12	GLY	GLY	ILE	ILE	29 - 308	3 - 282
24	12	12	GLY	GLY	ILE	ILE	29 - 308	3 - 282
25	13	13	TRP	TRP	PRO	PRO	30 - 310	4 - 284
26	13	13	TRP	TRP	PRO	PRO	30 - 310	4 - 284
27	14	14	GLY	GLY	PRO	PRO	29 - 311	3 - 285
28	14	14	GLY	GLY	PRO	PRO	29 - 311	3 - 285
29	15	15	TRP	TRP	PRO	PRO	30 - 310	4 - 284
30	15	15	TRP	TRP	PRO	PRO	30 - 310	4 - 284

NCS ensembles :

ID	Details
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6
4	Local NCS retraints between domains: 7 8
5	Local NCS retraints between domains: 9 10
6	Local NCS retraints between domains: 11 12
7	Local NCS retraints between domains: 13 14
8	Local NCS retraints between domains: 15 16
9	Local NCS retraints between domains: 17 18
10	Local NCS retraints between domains: 19 20
11	Local NCS retraints between domains: 21 22
12	Local NCS retraints between domains: 23 24
13	Local NCS retraints between domains: 25 26
14	Local NCS retraints between domains: 27 28
15	Local NCS retraints between domains: 29 30

#1: Protein	Uncharacterized protein TM_1410 Mass: 34836.691 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima MSB8 (bacteria) / Gene: TM_1410 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9X1D0
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 596 / Source method: isolated from a natural source / Formula: H₂O
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 grow	Temperature: 282 K / Method: vapor diffusion / Details: PEG MME 2000, Tris / PH range: 8-8.5

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

BESSY

/ Beamline: 14.1 / Wavelength: 0.9184 Å

Detector

Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 6, 2019

Radiation

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

Radiation wavelength

Wavelength: 0.9184 Å / Relative weight: 1

Reflection

Resolution: 2.6→49.262 Å / Num. obs: 171234 / % possible obs: 99.5 % / Redundancy: 4.3 % / CC_1/2: 0.978 / R_merge(I) obs: 0.194 / R_pim(I) all: 0.164 / R_rim(I) all: 0.255 / Net I/σ(I): 5.4

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all
14.24-49.21	4.2	0.076	1108	0.993	0.063	0.099
2.6-2.64	4.4	1.089	8538	0.36	0.922	1.433

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0425	refinement
REFMAC	5.8.0425	refinement
Aimless		data scaling
XDS		data reduction
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.6→49.262 Å / Cor.coef. F_o:F_c: 0.921 / Cor.coef. F_o:F_c free: 0.894 / SU B: 8.855 / SU ML: 0.172 / Cross valid method: FREE R-VALUE / ESU R: 0.215 / ESU R Free: 0.194
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2436	8591	5.018 %
R_work	0.2164	162629	-
all	0.218	-	-
obs	-	171220	99.325 %

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: 40.519 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.153 Å²	0 Å²	-0.965 Å²
2-	-	-0.477 Å²	0 Å²
3-	-	-	1.651 Å²

Refinement step

Cycle: LAST / Resolution: 2.6→49.262 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14037	0	0	596	14633

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.012	14444
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	13039
X-RAY DIFFRACTION	r_angle_refined_deg	2.358	1.809	19620
X-RAY DIFFRACTION	r_angle_other_deg	0.797	1.763	30055
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.43	5	1694
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	11.389	5	84
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.029	10	2387
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	15.135	10	789
X-RAY DIFFRACTION	r_chiral_restr	0.109	0.2	1987
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	17388
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	3544
X-RAY DIFFRACTION	r_nbd_refined	0.221	0.2	3117
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.203	0.2	12447
X-RAY DIFFRACTION	r_nbtor_refined	0.195	0.2	7172
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.092	0.2	7664
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.211	0.2	569
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.095	0.2	9
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.255	0.2	14
X-RAY DIFFRACTION	r_nbd_other	0.242	0.2	43
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.202	0.2	4
X-RAY DIFFRACTION	r_mcbond_it	5.595	3.875	6788
X-RAY DIFFRACTION	r_mcbond_other	5.595	3.875	6788
X-RAY DIFFRACTION	r_mcangle_it	7.989	6.956	8478
X-RAY DIFFRACTION	r_mcangle_other	7.99	6.956	8479
X-RAY DIFFRACTION	r_scbond_it	6.675	4.176	7656
X-RAY DIFFRACTION	r_scbond_other	6.675	4.176	7657
X-RAY DIFFRACTION	r_scangle_it	9.654	7.473	11142
X-RAY DIFFRACTION	r_scangle_other	9.654	7.474	11143
X-RAY DIFFRACTION	r_lrange_it	11.363	36.444	16933
X-RAY DIFFRACTION	r_lrange_other	11.354	36.447	16862
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.063	0.05	10092
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.062	0.05	9936
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.065	0.05	10058
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.063	0.05	10036
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.062	0.05	10004
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.062	0.05	9915
X-RAY DIFFRACTION	r_ncsr_local_group_7	0.059	0.05	10117
X-RAY DIFFRACTION	r_ncsr_local_group_8	0.06	0.05	10006
X-RAY DIFFRACTION	r_ncsr_local_group_9	0.057	0.05	10106
X-RAY DIFFRACTION	r_ncsr_local_group_10	0.063	0.05	9908
X-RAY DIFFRACTION	r_ncsr_local_group_11	0.06	0.05	9895
X-RAY DIFFRACTION	r_ncsr_local_group_12	0.056	0.05	9897
X-RAY DIFFRACTION	r_ncsr_local_group_13	0.065	0.05	9987
X-RAY DIFFRACTION	r_ncsr_local_group_14	0.057	0.05	10070
X-RAY DIFFRACTION	r_ncsr_local_group_15	0.064	0.05	9995

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	0.06316	0.0501
1	2	A	X-RAY DIFFRACTION	Local ncs	0.06316	0.0501
2	3	A	X-RAY DIFFRACTION	Local ncs	0.06217	0.0501
2	4	A	X-RAY DIFFRACTION	Local ncs	0.06217	0.0501
3	5	A	X-RAY DIFFRACTION	Local ncs	0.06451	0.0501
3	6	A	X-RAY DIFFRACTION	Local ncs	0.06451	0.0501
4	7	A	X-RAY DIFFRACTION	Local ncs	0.06301	0.0501
4	8	A	X-RAY DIFFRACTION	Local ncs	0.06301	0.0501
5	9	A	X-RAY DIFFRACTION	Local ncs	0.06194	0.0501
5	10	A	X-RAY DIFFRACTION	Local ncs	0.06194	0.0501
6	11	A	X-RAY DIFFRACTION	Local ncs	0.06172	0.0501
6	12	A	X-RAY DIFFRACTION	Local ncs	0.06172	0.0501
7	13	A	X-RAY DIFFRACTION	Local ncs	0.0589	0.0501
7	14	A	X-RAY DIFFRACTION	Local ncs	0.0589	0.0501
8	15	A	X-RAY DIFFRACTION	Local ncs	0.05995	0.0501
8	16	A	X-RAY DIFFRACTION	Local ncs	0.05995	0.0501
9	17	A	X-RAY DIFFRACTION	Local ncs	0.05675	0.0501
9	18	A	X-RAY DIFFRACTION	Local ncs	0.05675	0.0501
10	19	A	X-RAY DIFFRACTION	Local ncs	0.06329	0.0501
10	20	A	X-RAY DIFFRACTION	Local ncs	0.06329	0.0501
11	21	A	X-RAY DIFFRACTION	Local ncs	0.05992	0.0501
11	22	A	X-RAY DIFFRACTION	Local ncs	0.05992	0.0501
12	23	A	X-RAY DIFFRACTION	Local ncs	0.05648	0.0501
12	24	A	X-RAY DIFFRACTION	Local ncs	0.05648	0.0501
13	25	A	X-RAY DIFFRACTION	Local ncs	0.06548	0.0501
13	26	A	X-RAY DIFFRACTION	Local ncs	0.06548	0.0501
14	27	A	X-RAY DIFFRACTION	Local ncs	0.05671	0.0501
14	28	A	X-RAY DIFFRACTION	Local ncs	0.05671	0.0501
15	29	A	X-RAY DIFFRACTION	Local ncs	0.06421	0.0501
15	30	A	X-RAY DIFFRACTION	Local ncs	0.06421	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
2.6-2.667	0.364	579	0.343	12012	0.344	12653	0.911	0.918	99.51	0.344
2.667-2.74	0.342	558	0.327	11762	0.328	12359	0.923	0.929	99.6844	0.327
2.74-2.819	0.321	625	0.306	11340	0.307	11998	0.932	0.939	99.725	0.304
2.819-2.906	0.332	494	0.3	11037	0.301	11576	0.931	0.941	99.6113	0.297
2.906-3.001	0.315	467	0.284	10681	0.285	11279	0.932	0.946	98.8385	0.279
3.001-3.106	0.319	509	0.275	10201	0.277	10928	0.934	0.948	98.0051	0.266
3.106-3.222	0.259	470	0.239	10056	0.24	10539	0.953	0.961	99.8766	0.229
3.222-3.353	0.269	469	0.227	9682	0.229	10164	0.947	0.967	99.8721	0.216
3.353-3.502	0.248	508	0.224	9285	0.225	9811	0.964	0.973	99.8165	0.214
3.502-3.672	0.242	552	0.207	8696	0.209	9276	0.966	0.977	99.6981	0.2
3.672-3.869	0.224	502	0.195	8355	0.197	8926	0.971	0.979	99.227	0.19
3.869-4.102	0.206	498	0.175	7741	0.177	8403	0.972	0.982	98.0483	0.173
4.102-4.383	0.171	390	0.157	7512	0.157	7912	0.981	0.985	99.8736	0.161
4.383-4.731	0.171	397	0.141	6988	0.143	7400	0.981	0.986	99.7973	0.148
4.731-5.178	0.192	372	0.147	6432	0.15	6827	0.975	0.986	99.6631	0.156
5.178-5.781	0.219	377	0.189	5780	0.19	6198	0.973	0.983	99.3385	0.193
5.781-6.66	0.257	311	0.218	5110	0.22	5487	0.972	0.981	98.7972	0.222
6.66-8.12	0.207	207	0.188	4421	0.189	4655	0.976	0.981	99.42	0.198
8.12-11.331	0.204	198	0.18	3465	0.181	3701	0.972	0.978	98.9733	0.205
11.331-49.262	0.321	109	0.233	2073	0.238	2204	0.93	0.962	99.0018	0.272

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