PDB-9ep6: Alpha-Galactosaminidase family GH114 from Fusarium solani

ID or keywords:

Entry

Database: PDB / ID: 9ep6

Title

Alpha-Galactosaminidase family GH114 from Fusarium solani

Components

alpha-galactosidase

Keywords

HYDROLASE / family GH114 / Galactosaminogalactan degradation / GAG

Function / homology

Glycoside-hydrolase family GH114, TIM-barrel domain / Glycoside-hydrolase family GH114 / alpha-galactosidase / alpha-galactosidase activity / Aldolase-type TIM barrel / Glycoside hydrolase superfamily / DI(HYDROXYETHYL)ETHER / alpha-galactosidase

Function and homology information

Biological species

Fusarium solani (fungus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.61 Å

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.

Funding support

1items

Citation

Journal: Acta Crystallogr D Struct Biol / Year: 2025
Title: Structures of alpha-galactosaminidases from the CAZy GH114 family and homologs defining a new GH191 family of glycosidases.
Authors: Roth, C. / Moroz, O.V. / Miranda, S.A.D. / Jahn, L. / Blagova, E.V. / Lebedev, A.A. / Segura, D.R. / Stringer, M.A. / Friis, E.P. / Franco Cairo, J.P.L. / Davies, G.J. / Wilson, K.S.

History

Deposition	Mar 17, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Apr 23, 2025	Provider: repository / Type: Initial release
Revision 1.1	May 14, 2025	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	9ep6.cif.gz	806 KB	Display	PDBx/mmCIF format
PDB format	pdb9ep6.ent.gz	551.8 KB	Display	PDB format
PDBx/mmJSON format	9ep6.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ep/9ep6 ftp://data.pdbj.org/pub/pdb/validation_reports/ep/9ep6	HTTPS FTP

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Related structure data

Related structure data	9ep5C 9eux 9euz C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Experimental dataset #1	Data reference: 10.5281/zenodo.11011297 / Data set type: diffraction image data

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: alpha-galactosidase

B: alpha-galactosidase

C: alpha-galactosidase

hetero molecules

100 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: alpha-galactosidase

hetero molecules

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

2

B: alpha-galactosidase

hetero molecules

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

3

C: alpha-galactosidase

hetero molecules

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

Unit cell

Length a, b, c (Å)	95.569, 95.569, 231.428
Angle α, β, γ (deg.)	90, 90, 120
Int Tables number	152
Space group name H-M	P3₁21

Components on special symmetry positions

ID	Model	Components
1	1	C-825- HOH

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	A
3	2	A
4	2	A
5	3	A
6	3	A

NCS domain segments:

Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: TYR / End label comp-ID: TYR / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 31 - 317 / Label seq-ID: 10 - 296

Dom-ID	Component-ID	Ens-ID
1	1	1
2	1	1
3	2	2
4	2	2
5	3	3
6	3	3

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

#1: Protein	alpha-galactosidase Mass: 33185.977 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Fusarium solani (fungus) / Gene: NECHADRAFT_74418 / Production host: Aspergillus oryzae (mold) / References: UniProt: C7YJY3, alpha-galactosidase
#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 993 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
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: 3.06 Å³/Da / Density % sol: 59.86 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop Details: Index A6. 0.1 M Tris 8.5, 2 M ammonium sulphate, with 1 mM TEW, Anderson-Evans polyoxotungstate Jena Bioscience added to the protein prior to crystallisation. Microseed Matrix Seeding

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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 EIGER X 16M / Detector: PIXEL / Date: Jun 30, 2019

Radiation

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

Radiation wavelength

Wavelength: 0.9795 Å / Relative weight: 1

Reflection

Resolution: 1.61→82.77 Å / Num. obs: 158994 / % possible obs: 100 % / Redundancy: 12.2 % / B_iso Wilson estimate: 20.4 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.113 / R_pim(I) all: 0.049 / R_rim(I) all: 0.123 / Χ²: 0.94 / Net I/σ(I): 11.2

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	Χ²	% possible all
8.82-82.77	10.1	0.034	48.4	1129	0.998	0.015	0.037	0.72	99.8
1.61-1.64	12.1	2.346	1	7793	0.461	1.027	2.563	0.94	100

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Processing

Software

Name	Version	Classification
xia2		data reduction
XDS		data reduction
Aimless		data scaling
MOLREP		phasing
REFMAC	5.8.0425	refinement

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.61→82.765 Å / Cor.coef. F_o:F_c: 0.966 / Cor.coef. F_o:F_c free: 0.961 / SU B: 3.472 / SU ML: 0.059 / Cross valid method: FREE R-VALUE / ESU R: 0.075 / ESU R Free: 0.073
Details: Hydrogens have been added in their riding positions. The difference map indicates the presence of the fourth molecule in the asymmetric unit. If this molecule is modelled in the structure, ...

	R_factor	Num. reflection	% reflection
R_free	0.1951	8055	5.071 %
R_work	0.1778	150799	-
all	0.179	-	-
obs	-	158854	99.971 %

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: 29.115 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.315 Å²	0.158 Å²	-0 Å²
2-	-	0.315 Å²	0 Å²
3-	-	-	-1.022 Å²

Refinement step

Cycle: LAST / Resolution: 1.61→82.765 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6785	0	48	993	7826

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.012	7150
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.016	6411
X-RAY DIFFRACTION	r_angle_refined_deg	1.696	1.812	9725
X-RAY DIFFRACTION	r_angle_other_deg	0.652	1.78	14942
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.202	5	888
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	7.081	5	15
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.068	10	1158
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	15.272	10	339
X-RAY DIFFRACTION	r_chiral_restr	0.094	0.2	1002
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	8444
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	1532
X-RAY DIFFRACTION	r_nbd_refined	0.212	0.2	1327
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.173	0.2	5984
X-RAY DIFFRACTION	r_nbtor_refined	0.178	0.2	3493
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.076	0.2	3408
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.154	0.2	751
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.009	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.116	0.2	19
X-RAY DIFFRACTION	r_nbd_other	0.145	0.2	100
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.129	0.2	45
X-RAY DIFFRACTION	r_mcbond_it	1.686	1.541	3516
X-RAY DIFFRACTION	r_mcbond_other	1.686	1.541	3516
X-RAY DIFFRACTION	r_mcangle_it	2.508	2.764	4416
X-RAY DIFFRACTION	r_mcangle_other	2.508	2.764	4417
X-RAY DIFFRACTION	r_scbond_it	2.554	1.818	3634
X-RAY DIFFRACTION	r_scbond_other	2.554	1.818	3635
X-RAY DIFFRACTION	r_scangle_it	3.955	3.198	5309
X-RAY DIFFRACTION	r_scangle_other	3.955	3.199	5310
X-RAY DIFFRACTION	r_lrange_it	6.536	18.826	8370
X-RAY DIFFRACTION	r_lrange_other	6.394	17.167	8056
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.083	0.05	9536
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.074	0.05	9587
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.062	0.05	9728

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	0.08286	0.05009
1	2	A	X-RAY DIFFRACTION	Local ncs	0.08286	0.05009
2	3	A	X-RAY DIFFRACTION	Local ncs	0.07436	0.05009
2	4	A	X-RAY DIFFRACTION	Local ncs	0.07436	0.05009
3	5	A	X-RAY DIFFRACTION	Local ncs	0.06184	0.0501
3	6	A	X-RAY DIFFRACTION	Local ncs	0.06184	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
1.61-1.652	0.325	600	0.315	11043	0.315	11652	0.923	0.928	99.9228	0.316
1.652-1.697	0.302	554	0.298	10761	0.298	11324	0.942	0.941	99.9205	0.296
1.697-1.746	0.267	546	0.262	10457	0.262	11008	0.951	0.957	99.9546	0.252
1.746-1.8	0.255	549	0.243	10199	0.244	10755	0.962	0.965	99.9349	0.229
1.8-1.859	0.242	509	0.212	9828	0.213	10338	0.964	0.973	99.9903	0.195
1.859-1.924	0.207	469	0.197	9628	0.197	10099	0.975	0.976	99.9802	0.178
1.924-1.997	0.194	516	0.17	9208	0.171	9724	0.977	0.982	100	0.152
1.997-2.078	0.198	519	0.169	8847	0.17	9369	0.976	0.983	99.968	0.153
2.078-2.171	0.175	474	0.153	8542	0.154	9017	0.981	0.986	99.9889	0.141
2.171-2.276	0.169	503	0.148	8096	0.149	8602	0.982	0.987	99.9651	0.136
2.276-2.4	0.169	425	0.143	7757	0.145	8182	0.983	0.988	100	0.132
2.4-2.545	0.176	377	0.143	7367	0.144	7744	0.982	0.988	100	0.132
2.545-2.72	0.179	365	0.156	6988	0.157	7353	0.981	0.985	100	0.145
2.72-2.938	0.196	335	0.168	6483	0.169	6818	0.976	0.984	100	0.159
2.938-3.218	0.191	311	0.184	6000	0.185	6311	0.979	0.982	100	0.176
3.218-3.597	0.205	282	0.176	5443	0.177	5725	0.978	0.983	100	0.167
3.597-4.153	0.166	257	0.151	4860	0.152	5117	0.984	0.987	100	0.141
4.153-5.083	0.154	210	0.153	4115	0.153	4325	0.988	0.988	100	0.141
5.083-7.174	0.222	179	0.213	3243	0.214	3422	0.978	0.981	100	0.203
7.174-82.765	0.246	75	0.239	1934	0.239	2015	0.963	0.964	99.7022	0.21

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	1.1626	-0.2903	-0.524	1.765	-0.2762	1.7758	0.0121	0.1495	0.0468	-0.0964	0.0139	0.0801	0.0943	-0.1314	-0.026	0.0715	0.0296	-0.0016	0.1011	0.0224	0.0561	-2.7953	86.5735	-15.4118
2	1.3114	-0.4508	0.1367	1.0447	0.0433	1.1955	-0.0109	-0.0607	0.0301	0.0622	0.0401	0.0427	-0.0401	-0.0018	-0.0292	0.1196	0.0219	0.0292	0.0384	0.0056	0.0271	0.5578	79.3377	20.7303
3	1.5868	-0.0462	-0.0875	0.6128	0.2509	1.2033	0.007	-0.0956	-0.0265	0.0359	0.02	-0.0208	-0.018	0.0953	-0.027	0.0481	0.0352	-0.0016	0.0753	0.0053	0.0029	31.1805	45.3741	18.2017

Refinement TLS group

Selection: ALL

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