PDB-9eux: Glycoside hydrolase familiy 191 enzyme from Thermotoga maritima

ID or keywords:

Entry

Database: PDB / ID: 9eux

Title

Glycoside hydrolase familiy 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: 2.4 Å

Authors

Roth, C.

Funding support

Germany, 1items

Citation

Journal: To Be Published
Title: Structures of alpha-galactosaminidases from the GH114 family
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: Structure summary / Category: struct / Item: _struct.title

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9eux.cif.gz	674.6 KB	Display	PDBx/mmCIF format
PDB format	pdb9eux.ent.gz	551.2 KB	Display	PDB format
PDBx/mmJSON format	9eux.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/9eux ftp://data.pdbj.org/pub/pdb/validation_reports/eu/9eux	HTTPS FTP

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Related structure data

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

G: Uncharacterized protein TM_1410

E: Uncharacterized protein TM_1410

C: Uncharacterized protein TM_1410

D: Uncharacterized protein TM_1410

B: Uncharacterized protein TM_1410

A: Uncharacterized protein TM_1410

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

1

G: Uncharacterized protein TM_1410

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

2

E: Uncharacterized protein TM_1410

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

3

C: Uncharacterized protein TM_1410

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

4

D: Uncharacterized protein TM_1410

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

5

B: Uncharacterized protein TM_1410

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

6

A: Uncharacterized protein TM_1410

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

Unit cell

Length a, b, c (Å)	195.186, 84.497, 195.482
Angle α, β, γ (deg.)	90, 119.914, 90
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Auth asym-ID: G / 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	GLN	GLN	29 - 309	29 - 309
2	1	1	GLY	GLY	GLN	GLN	29 - 309	29 - 309
3	2	2	TRP	TRP	PRO	PRO	30 - 310	30 - 310
4	2	2	TRP	TRP	PRO	PRO	30 - 310	30 - 310
5	3	3	PHE	PHE	GLN	GLN	31 - 309	31 - 309
6	3	3	PHE	PHE	GLN	GLN	31 - 309	31 - 309
7	4	4	GLU	GLU	PRO	PRO	28 - 311	28 - 311
8	4	4	GLU	GLU	PRO	PRO	28 - 311	28 - 311
9	5	5	GLY	GLY	PRO	PRO	29 - 310	29 - 310
10	5	5	GLY	GLY	PRO	PRO	29 - 310	29 - 310
11	6	6	TRP	TRP	GLN	GLN	30 - 309	30 - 309
12	6	6	TRP	TRP	GLN	GLN	30 - 309	30 - 309
13	7	7	PHE	PHE	GLN	GLN	31 - 309	31 - 309
14	7	7	PHE	PHE	GLN	GLN	31 - 309	31 - 309
15	8	8	GLY	GLY	GLN	GLN	29 - 309	29 - 309
16	8	8	GLY	GLY	GLN	GLN	29 - 309	29 - 309
17	9	9	GLY	GLY	GLN	GLN	29 - 309	29 - 309
18	9	9	GLY	GLY	GLN	GLN	29 - 309	29 - 309
19	10	10	PHE	PHE	GLN	GLN	31 - 309	31 - 309
20	10	10	PHE	PHE	GLN	GLN	31 - 309	31 - 309
21	11	11	TRP	TRP	PRO	PRO	30 - 310	30 - 310
22	11	11	TRP	TRP	PRO	PRO	30 - 310	30 - 310
23	12	12	TRP	TRP	PRO	PRO	30 - 310	30 - 310
24	12	12	TRP	TRP	PRO	PRO	30 - 310	30 - 310
25	13	13	PHE	PHE	GLN	GLN	31 - 309	31 - 309
26	13	13	PHE	PHE	GLN	GLN	31 - 309	31 - 309
27	14	14	PHE	PHE	GLN	GLN	31 - 309	31 - 309
28	14	14	PHE	PHE	GLN	GLN	31 - 309	31 - 309
29	15	15	GLY	GLY	PRO	PRO	29 - 310	29 - 310
30	15	15	GLY	GLY	PRO	PRO	29 - 310	29 - 310

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: 37752.258 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) / Strain (production host): Gold / References: UniProt: Q9X1D0
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 540 / 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: 292 K / Method: vapor diffusion / Details: PEG MME 2000, Tris / PH range: 8.0-8.5

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

PETRA III, DESY

/ Beamline: P11 / Wavelength: 1.0332 Å

Detector

Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 7, 2018

Radiation

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

Radiation wavelength

Wavelength: 1.0332 Å / Relative weight: 1

Reflection

Resolution: 2.4→48.945 Å / Num. obs: 216213 / % possible obs: 100 % / Redundancy: 6.9 % / CC_1/2: 0.985 / R_merge(I) obs: 0.183 / R_pim(I) all: 0.115 / R_rim(I) all: 0.217 / Net I/σ(I): 6.4

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
13.15-48.9	6.7	0.071	1414	0.968	0.045	0.084
2.4-2.44	7	1.933	10715	0.412	1.194	2.277

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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: 2.4→48.945 Å / Cor.coef. F_o:F_c: 0.919 / Cor.coef. F_o:F_c free: 0.901 / SU B: 8.081 / SU ML: 0.175 / Cross valid method: FREE R-VALUE / ESU R: 0.183 / ESU R Free: 0.172
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2639	11162	5.163 %
R_work	0.2364	205033	-
all	0.238	-	-
obs	-	216195	99.936 %

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: 53.804 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.235 Å²	0 Å²	-0.097 Å²
2-	-	-2.17 Å²	0 Å²
3-	-	-	0.63 Å²

Refinement step

Cycle: LAST / Resolution: 2.4→48.945 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14028	0	0	540	14568

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.012	14493
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	13089
X-RAY DIFFRACTION	r_angle_refined_deg	2.118	1.81	19693
X-RAY DIFFRACTION	r_angle_other_deg	0.775	1.764	30166
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.875	5	1703
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	13.969	5	86
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.381	10	2399
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	15.305	10	793
X-RAY DIFFRACTION	r_chiral_restr	0.111	0.2	1993
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	17483
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	3565
X-RAY DIFFRACTION	r_nbd_refined	0.225	0.2	3226
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.209	0.2	12564
X-RAY DIFFRACTION	r_nbtor_refined	0.194	0.2	7078
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.084	0.2	7333
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.211	0.2	592
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.126	0.2	11
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.274	0.2	13
X-RAY DIFFRACTION	r_nbd_other	0.238	0.2	41
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.09	0.2	8
X-RAY DIFFRACTION	r_mcbond_it	7.355	5.197	6809
X-RAY DIFFRACTION	r_mcbond_other	7.355	5.197	6809
X-RAY DIFFRACTION	r_mcangle_it	9.8	9.331	8513
X-RAY DIFFRACTION	r_mcangle_other	9.799	9.332	8514
X-RAY DIFFRACTION	r_scbond_it	8.562	5.513	7684
X-RAY DIFFRACTION	r_scbond_other	8.562	5.513	7685
X-RAY DIFFRACTION	r_scangle_it	11.513	9.942	11180
X-RAY DIFFRACTION	r_scangle_other	11.512	9.942	11181
X-RAY DIFFRACTION	r_lrange_it	13.38	49.817	17033
X-RAY DIFFRACTION	r_lrange_other	13.392	49.844	16974
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.094	0.05	9795
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.094	0.05	9748
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.096	0.05	9700
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.099	0.05	9864
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.087	0.05	9862
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.102	0.05	9671
X-RAY DIFFRACTION	r_ncsr_local_group_7	0.094	0.05	9669
X-RAY DIFFRACTION	r_ncsr_local_group_8	0.099	0.05	9805
X-RAY DIFFRACTION	r_ncsr_local_group_9	0.083	0.05	9842
X-RAY DIFFRACTION	r_ncsr_local_group_10	0.102	0.05	9587
X-RAY DIFFRACTION	r_ncsr_local_group_11	0.091	0.05	9857
X-RAY DIFFRACTION	r_ncsr_local_group_12	0.092	0.05	9773
X-RAY DIFFRACTION	r_ncsr_local_group_13	0.101	0.05	9665
X-RAY DIFFRACTION	r_ncsr_local_group_14	0.087	0.05	9779
X-RAY DIFFRACTION	r_ncsr_local_group_15	0.089	0.05	9842

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	G	X-RAY DIFFRACTION	Local ncs	0.09365	0.05009
1	2	G	X-RAY DIFFRACTION	Local ncs	0.09365	0.05009
2	3	G	X-RAY DIFFRACTION	Local ncs	0.0937	0.05009
2	4	G	X-RAY DIFFRACTION	Local ncs	0.0937	0.05009
3	5	G	X-RAY DIFFRACTION	Local ncs	0.09641	0.0501
3	6	G	X-RAY DIFFRACTION	Local ncs	0.09641	0.0501
4	7	G	X-RAY DIFFRACTION	Local ncs	0.09855	0.05009
4	8	G	X-RAY DIFFRACTION	Local ncs	0.09855	0.05009
5	9	G	X-RAY DIFFRACTION	Local ncs	0.08747	0.05009
5	10	G	X-RAY DIFFRACTION	Local ncs	0.08747	0.05009
6	11	G	X-RAY DIFFRACTION	Local ncs	0.10238	0.05009
6	12	G	X-RAY DIFFRACTION	Local ncs	0.10238	0.05009
7	13	G	X-RAY DIFFRACTION	Local ncs	0.09449	0.0501
7	14	G	X-RAY DIFFRACTION	Local ncs	0.09449	0.0501
8	15	G	X-RAY DIFFRACTION	Local ncs	0.09868	0.0501
8	16	G	X-RAY DIFFRACTION	Local ncs	0.09868	0.0501
9	17	G	X-RAY DIFFRACTION	Local ncs	0.08274	0.05009
9	18	G	X-RAY DIFFRACTION	Local ncs	0.08274	0.05009
10	19	G	X-RAY DIFFRACTION	Local ncs	0.1018	0.05009
10	20	G	X-RAY DIFFRACTION	Local ncs	0.1018	0.05009
11	21	G	X-RAY DIFFRACTION	Local ncs	0.09131	0.05009
11	22	G	X-RAY DIFFRACTION	Local ncs	0.09131	0.05009
12	23	G	X-RAY DIFFRACTION	Local ncs	0.09194	0.05009
12	24	G	X-RAY DIFFRACTION	Local ncs	0.09194	0.05009
13	25	G	X-RAY DIFFRACTION	Local ncs	0.1005	0.05009
13	26	G	X-RAY DIFFRACTION	Local ncs	0.1005	0.05009
14	27	G	X-RAY DIFFRACTION	Local ncs	0.08691	0.05009
14	28	G	X-RAY DIFFRACTION	Local ncs	0.08691	0.05009
15	29	G	X-RAY DIFFRACTION	Local ncs	0.08932	0.05009
15	30	G	X-RAY DIFFRACTION	Local ncs	0.08932	0.05009

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
2.4-2.462	0.365	828	0.341	15033	0.342	15898	0.891	0.899	99.7673	0.344
2.462-2.529	0.344	675	0.328	14788	0.329	15463	0.907	0.912	100	0.331
2.529-2.602	0.362	775	0.325	14289	0.327	15064	0.907	0.924	100	0.328
2.602-2.682	0.344	838	0.315	13725	0.317	14563	0.918	0.932	100	0.316
2.682-2.77	0.322	774	0.286	13445	0.288	14219	0.922	0.946	100	0.283
2.77-2.867	0.312	761	0.273	12908	0.275	13669	0.932	0.948	100	0.267
2.867-2.975	0.294	717	0.254	12540	0.256	13257	0.945	0.957	100	0.246
2.975-3.096	0.253	767	0.223	11993	0.225	12760	0.958	0.966	100	0.213
3.096-3.233	0.237	604	0.217	11731	0.218	12335	0.961	0.968	100	0.207
3.233-3.39	0.277	623	0.234	11046	0.236	11669	0.947	0.965	100	0.226
3.39-3.572	0.27	429	0.23	10672	0.232	11101	0.953	0.968	100	0.226
3.572-3.788	0.258	516	0.228	10092	0.23	10608	0.955	0.969	100	0.228
3.788-4.048	0.241	531	0.216	9415	0.218	9946	0.963	0.97	100	0.219
4.048-4.369	0.209	395	0.196	8842	0.197	9237	0.971	0.973	100	0.203
4.369-4.783	0.219	492	0.191	8096	0.192	8588	0.964	0.973	100	0.2
4.783-5.341	0.237	357	0.211	7416	0.213	7773	0.962	0.97	100	0.219
5.341-6.155	0.251	348	0.231	6533	0.232	6881	0.961	0.967	100	0.237
6.155-7.508	0.286	309	0.257	5550	0.258	5859	0.946	0.959	100	0.263
7.508-10.496	0.229	285	0.219	4318	0.22	4603	0.958	0.962	100	0.234
10.496-48.945	0.265	138	0.239	2601	0.241	2740	0.946	0.959	99.9635	0.264

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