PDB-12nt: Crystal structure of a GH26 enzyme (EiGH26a) in complex with Gluc...

ID or keywords:

Entry

Database: PDB / ID: 12nt

Title

Crystal structure of a GH26 enzyme (EiGH26a) in complex with Glucose-beta-1,4-Mannose

Components

Glycoside hydrolase family 26

Keywords

HYDROLASE / metagenome / manatee / gut microbiota / heteromannan

Function / homology

TRIETHYLENE GLYCOL

Function and homology information

Biological species

metagenome (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.2 Å

Authors

Miyamoto, R.Y. / Oliveira, C.H.M. / Morao, L.G. / Martins, M.P. / Murakami, M.T.

Funding support

Brazil, 5items

Organization	Grant number	Country
Sao Paulo Research Foundation (FAPESP)	2021/04891-3	Brazil
Sao Paulo Research Foundation (FAPESP)	2022/03059-5	Brazil
Sao Paulo Research Foundation (FAPESP)	2021/09793-0	Brazil
Brazilian National Council for Scientific and Technological Development (CNPq)	303898/2024-0	Brazil
Brazilian National Council for Scientific and Technological Development (CNPq)	304440/2024-8	Brazil

Citation

Journal: To Be Published
Title: Crystal structure of a GH26 enzyme (EiGH26a) in complex with Glucose-beta-1,4-Mannose
Authors: Persinoti, G.F. / Martins, M.P. / Silva, C.B.C. / Streit, R.S.A. / Paixao, D.A.A. / Martins, G.H. / Higasi, P.M.R. / Braatz, G.M. / Silva, M.K.P. / Morao, L.G. / Martins-Junior, J. / ...

History

Deposition	Apr 13, 2026	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 9, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	12nt.cif.gz	153.4 KB	Display	PDBx/mmCIF format
PDB format	pdb12nt.ent.gz	116.6 KB	Display	PDB format
PDBx/mmJSON format	12nt.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/2n/12nt ftp://data.pdbj.org/pub/pdb/validation_reports/2n/12nt	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

A: Glycoside hydrolase family 26

hetero molecules

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

1

A: Glycoside hydrolase family 26

hetero molecules

A: Glycoside hydrolase family 26

hetero molecules

defined by author&software
Evidence: gel filtration
79.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	67.375, 65.116, 84.385
Angle α, β, γ (deg.)	90.00, 111.34, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	A-725- HOH
2	1	A-737- HOH

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein

Glycoside hydrolase family 26

Mass: 39306.363 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) metagenome (others) / Production host:

Escherichia coli BL21(DE3) (bacteria)

#2: Polysaccharide

beta-D-glucopyranose-(1-4)-beta-D-mannopyranose

Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Non-polymers , 4 types, 245 molecules

#3: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical	ChemComp-PGE / TRIETHYLENE GLYCOL Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₁₄O₄
#5: Chemical	ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₂NO₃ / Comment: pH buffer*YM
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 241 / 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: 2.19 Å³/Da / Density % sol: 43.92 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.2M magnesium chloride hexahydrate; 0.1M tris hydrochloride pH 8.5; 30% (w/v) PEG 4000

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site: LNLS SIRIUS / Beamline: MANACA / Wavelength: 0.9772 Å

Detector

Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 24, 2025

Radiation

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

Radiation wavelength

Wavelength: 0.9772 Å / Relative weight: 1

Reflection

Resolution: 1.2→45.19 Å / Num. obs: 101455 / % possible obs: 96.9 % / Redundancy: 6.6 % / CC_1/2: 0.998 / R_merge(I) obs: 0.036 / R_rim(I) all: 0.049 / Net I/σ(I): 6.92

Reflection shell

Resolution (Å)	R_merge(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	Diffraction-ID
1.2-1.28	0.767	6273	0.407	1.085	1
1.28-1.37	0.426	7076	0.67	0.603	1
1.37-1.48	0.256	7136	0.844	0.363	1
1.48-1.62	0.138	6536	0.953	0.194	1
1.62-1.81	0.078	5534	0.982	0.11	1
1.81-2.09	0.046	4954	0.994	0.062	1
2.09-2.55	0.034	3843	0.995	0.046	1
2.55-3.6	0.027	2537	0.997	0.037	1
3.6-45.19	0.021	1414	0.998	0.026	1

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Processing

Software

Name	Version	Classification
PHENIX	1.20.1_4487	refinement
XDS		data scaling
PDB_EXTRACT		data extraction
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.2→45.19 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.4 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1667	5072	5 %
R_work	0.1581	-	-
obs	0.1585	101455	96.92 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.2→45.19 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2618	0	43	241	2902

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	2774
X-RAY DIFFRACTION	f_angle_d	0.79	3771
X-RAY DIFFRACTION	f_dihedral_angle_d	11.426	996
X-RAY DIFFRACTION	f_chiral_restr	0.075	393
X-RAY DIFFRACTION	f_plane_restr	0.007	477

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.2-1.22	0.2992	153	0.3062	2886	X-RAY DIFFRACTION	89
1.22-1.23	0.3077	167	0.294	3188	X-RAY DIFFRACTION	95
1.23-1.25	0.3077	162	0.2799	3081	X-RAY DIFFRACTION	94
1.25-1.26	0.2499	166	0.2701	3167	X-RAY DIFFRACTION	95
1.26-1.28	0.2479	165	0.2553	3124	X-RAY DIFFRACTION	95
1.28-1.3	0.2748	167	0.2432	3178	X-RAY DIFFRACTION	95
1.3-1.32	0.2788	164	0.2309	3121	X-RAY DIFFRACTION	95
1.32-1.34	0.2195	168	0.2204	3195	X-RAY DIFFRACTION	96
1.34-1.36	0.1892	165	0.2071	3130	X-RAY DIFFRACTION	96
1.36-1.38	0.2212	171	0.2031	3240	X-RAY DIFFRACTION	96
1.38-1.4	0.214	165	0.1959	3140	X-RAY DIFFRACTION	96
1.4-1.43	0.1939	167	0.1975	3185	X-RAY DIFFRACTION	96
1.43-1.46	0.2238	169	0.1886	3194	X-RAY DIFFRACTION	97
1.46-1.49	0.1971	167	0.1814	3182	X-RAY DIFFRACTION	97
1.49-1.52	0.1861	171	0.1599	3251	X-RAY DIFFRACTION	97
1.52-1.55	0.1761	169	0.1555	3201	X-RAY DIFFRACTION	97
1.55-1.59	0.1741	169	0.153	3218	X-RAY DIFFRACTION	97
1.59-1.64	0.1772	170	0.1463	3240	X-RAY DIFFRACTION	98
1.64-1.68	0.1518	170	0.1464	3221	X-RAY DIFFRACTION	98
1.68-1.74	0.1429	172	0.1453	3266	X-RAY DIFFRACTION	98
1.74-1.8	0.1418	171	0.1401	3250	X-RAY DIFFRACTION	98
1.8-1.87	0.1538	172	0.1424	3274	X-RAY DIFFRACTION	98
1.87-1.96	0.1352	171	0.1354	3240	X-RAY DIFFRACTION	99
1.96-2.06	0.1341	172	0.1373	3276	X-RAY DIFFRACTION	99
2.06-2.19	0.139	172	0.133	3272	X-RAY DIFFRACTION	99
2.19-2.36	0.1501	175	0.1438	3325	X-RAY DIFFRACTION	99
2.36-2.6	0.1837	173	0.1487	3300	X-RAY DIFFRACTION	99
2.6-2.97	0.1745	174	0.1531	3294	X-RAY DIFFRACTION	99
2.97-3.74	0.1505	175	0.148	3340	X-RAY DIFFRACTION	100
3.74-45.19	0.1433	180	0.1447	3404	X-RAY DIFFRACTION	99

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	0.1285	0.0642	-0.2697	2.3592	1.8085	3.6677	0.0136	0.0254	0.0378	-0.0451	-0.1272	0.2075	-0.1265	-0.2029	0.0964	0.0756	0.0005	-0.0056	0.111	-0.0111	0.1368	-3.898	1.9827	27.4143
2	1.3294	1.8131	-0.2914	6.9091	1.1714	3.6525	-0.0538	0.0446	-0.1528	0.1249	0.0075	-0.0109	0.1862	-0.2196	0.0715	0.116	-0.0312	0.0035	0.1204	-0.0092	0.1428	-8.4762	-14.2636	24.0187
3	0.2707	0.0663	-0.2993	0.2769	0.2143	1.646	0.0415	0.0318	0.0339	-0.0078	-0.0117	0.0155	0.0281	-0.0729	-0.0141	0.1226	0.0048	-0.0065	0.1095	0.0045	0.1082	-0.5937	-5.0623	12.0475
4	2.1674	2.4375	1.0971	4.8134	0.8572	1.7378	0.0646	0.0835	-0.1995	0.0145	0.0163	-0.274	0.0793	0.2803	-0.0674	0.1125	0.0177	0.0278	0.1996	-0.0101	0.1357	18.8308	-1.7638	7.2011
5	0.7593	0.0754	0.1416	0.2682	0.167	1.4485	0.015	0.0922	0.0303	-0.0423	0.0044	0.0175	-0.0456	0.0178	-0.0208	0.1235	-0.0017	-0.0026	0.1049	0.0049	0.1092	5.6451	2.0291	10.9442
6	2.9703	0.4208	0.5691	2.9731	-0.0445	2.787	0.0025	0.0306	0.0488	0.005	0.0184	-0.1961	-0.1653	0.3112	0.0043	0.0992	-0.0335	0.0177	0.114	-0.0063	0.0614	16.8839	6.406	14.6962
7	2.426	-0.9255	1.2656	1.5569	-1.0054	2.0837	-0.0224	0.0539	0.1448	0.0382	0.0017	-0.0508	-0.1494	0.1318	0.052	0.1313	-0.014	0.0118	0.0897	-0.009	0.0963	10.29	7.9059	21.3352
8	1.5962	-0.1015	0.0082	4.968	0.5398	1.8482	0.0142	-0.1314	0.0762	0.0713	0.0299	-0.0782	-0.0761	0.0904	-0.0334	0.0865	-0.0099	0.0089	0.0983	-0.0057	0.0647	9.6716	1.9434	32.1235
9	2.1554	1.273	0.1469	5.5833	-0.28	0.8174	0.0018	-0.0818	-0.1357	0.2101	-0.0228	-0.1129	0.1599	0.0898	0.0084	0.1329	0.0112	-0.0151	0.0985	0.0271	0.0783	6.3841	-12.592	37.8816
10	1.3751	-0.0577	-0.2949	2.1184	0.1042	1.2674	0.0238	-0.0262	0.0101	0.0865	0.0014	0.1742	0.1351	-0.1225	-0.0188	0.1292	-0.0168	-0.0037	0.105	0.0024	0.1016	-4.8496	-7.6957	32.9963

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 31 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 32 through 48 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 49 through 94 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 95 through 123 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 124 through 162 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 163 through 190 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 191 through 224 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 225 through 261 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 262 through 285 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 286 through 323 )

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