PDB-24te: Crystal structure of GH30 Streptomyces avermitilis endo-beta-1,6-...

ID or keywords:

Entry

Database: PDB / ID: 24te

Title

Crystal structure of GH30 Streptomyces avermitilis endo-beta-1,6-galactanase complexed with Gal-beta1,6-Gal

Components

Secreted endo-beta-1,6-galactanase

Keywords

HYDROLASE / glycoside hydrolase family 30

Function / homology

Endo-beta-1,6-galactanase/Exo-beta-1,6-galactobiohydrolase / hydrolase activity, hydrolyzing O-glycosyl compounds / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Glycoside hydrolase superfamily / Secreted endo-beta-1,6-galactanase

Function and homology information

Biological species

Streptomyces avermitilis MA-4680 = NBRC 14893 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2 Å

Authors

Fujimoto, Z. / Kishine, N. / Kaneko, S.

Funding support

1items

Citation

Journal: Acta Crystallogr D Struct Biol / Year: 2026
Title: Crystal structure of endo-beta-1,6-galactanase from Streptomyces avermitilis.
Authors: Fujimoto, Z. / Kishine, N. / Kotake, T. / Kaneko, S.

History

Deposition	Mar 19, 2026	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Aug 12, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	24te.cif.gz	114.7 KB	Display	PDBx/mmCIF format
PDB format	pdb24te.ent.gz	81.3 KB	Display	PDB format
PDBx/mmJSON format	24te.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/4t/24te ftp://data.pdbj.org/pub/pdb/validation_reports/4t/24te	HTTPS FTP

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Related structure data

Related structure data	24tdC 24tfC 24tgC C: citing same article (ref.)
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	#220 - Apr 2018 Dehalogenases similarity (2) #111 - Mar 2009 Hydrogenase similarity (2)

Deposited unit

A: Secreted endo-beta-1,6-galactanase

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	50.245, 50.245, 330.781
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	96
Space group name H-M	P4₃2₁2

Components on special symmetry positions

ID	Model	Components
1	1	A-803- HOH
2	1	A-920- HOH

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Protein / Sugars , 2 types, 3 molecules A

#1: Protein

Secreted endo-beta-1,6-galactanase

Mass: 52293.719 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Streptomyces avermitilis MA-4680 = NBRC 14893 (bacteria)
Gene: SAVERM_5205 / Production host:

Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q82CY3

#2: Polysaccharide

beta-D-galactopyranose-(1-6)-beta-D-galactopyranose

Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 2 / Source method: obtained synthetically

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Non-polymers , 4 types, 228 molecules

#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO₄
#4: Chemical	ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₁₃NO₄S / Comment: pH buffer*YM
#5: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 224 / 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: 2.03 Å³/Da / Density % sol: 39.4 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 1.6 M ammonium sulfate, 0.1 M MES pH 6.5, 10% dioxane

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Data collection

Diffraction	Mean temperature: 95 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 25, 2013
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2→100 Å / Num. obs: 29929 / % possible obs: 98.6 % / Redundancy: 19.6 % / R_merge(I) obs: 0.174 / Net I/σ(I): 13.3
Reflection shell	Resolution: 2→2.07 Å / R_merge(I) obs: 0.907 / Mean I/σ(I) obs: 4 / Num. unique obs: 2914

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0431	refinement
HKL-2000		data reduction
SCALEPACK		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2→49.675 Å / Cor.coef. F_o:F_c: 0.961 / Cor.coef. F_o:F_c free: 0.912 / SU B: 4.307 / SU ML: 0.117 / Cross valid method: THROUGHOUT / ESU R: 0.196 / ESU R Free: 0.177
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2344	1507	5.063 %	RANDOM
R_work	0.1754	28257	-	-
all	0.178	-	-	-
obs	-	29764	98.625 %	-

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: 31.483 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.084 Å²	-0 Å²	0 Å²
2-	-	-0.084 Å²	-0 Å²
3-	-	-	0.168 Å²

Refinement step

Cycle: LAST / Resolution: 2→49.675 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3547	0	74	224	3845

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.006	0.012	3716
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	3292
X-RAY DIFFRACTION	r_angle_refined_deg	1.452	1.766	5084
X-RAY DIFFRACTION	r_angle_other_deg	0.549	1.732	7546
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.409	5	465
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	6.224	5	21
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.196	10	515
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	15.333	10	157
X-RAY DIFFRACTION	r_chiral_restr	0.072	0.2	570
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	4513
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	923
X-RAY DIFFRACTION	r_nbd_refined	0.198	0.2	766
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.207	0.2	3124
X-RAY DIFFRACTION	r_nbtor_refined	0.181	0.2	1877
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.081	0.2	1843
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.146	0.2	240
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.133	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.111	0.2	12
X-RAY DIFFRACTION	r_nbd_other	0.176	0.2	57
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.138	0.2	31
X-RAY DIFFRACTION	r_mcbond_it	2.325	3.234	1863
X-RAY DIFFRACTION	r_mcbond_other	2.325	3.235	1863
X-RAY DIFFRACTION	r_mcangle_it	2.981	5.802	2327
X-RAY DIFFRACTION	r_mcangle_other	2.983	5.805	2328
X-RAY DIFFRACTION	r_scbond_it	2.836	3.485	1853
X-RAY DIFFRACTION	r_scbond_other	2.836	3.486	1854
X-RAY DIFFRACTION	r_scangle_it	4.029	6.31	2757
X-RAY DIFFRACTION	r_scangle_other	4.028	6.311	2758
X-RAY DIFFRACTION	r_lrange_it	5.01	34.253	4352
X-RAY DIFFRACTION	r_lrange_other	4.985	33.042	4313

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	0.289	89	0.246	2060	0.248	2149	0.951	0.959	100	0.202
2.052-2.108	0.271	100	0.237	2040	0.239	2140	0.954	0.964	100	0.191
2.108-2.169	0.279	102	0.221	1941	0.224	2044	0.952	0.971	99.9511	0.189
2.169-2.236	0.278	102	0.203	1900	0.206	2002	0.945	0.973	100	0.172
2.236-2.309	0.228	105	0.171	1839	0.174	1944	0.968	0.981	100	0.145
2.309-2.39	0.259	118	0.17	1794	0.175	1914	0.957	0.981	99.8955	0.146
2.39-2.48	0.235	86	0.168	1706	0.171	1793	0.964	0.981	99.9442	0.145
2.48-2.581	0.226	80	0.165	1673	0.168	1756	0.966	0.982	99.8292	0.144
2.581-2.695	0.222	81	0.163	1619	0.166	1703	0.965	0.984	99.8238	0.145
2.695-2.826	0.242	80	0.176	1553	0.179	1636	0.966	0.981	99.8166	0.162
2.826-2.978	0.258	72	0.177	1476	0.18	1567	0.964	0.982	98.7875	0.172
2.978-3.158	0.231	84	0.171	1358	0.175	1461	0.97	0.982	98.6995	0.174
3.158-3.376	0.231	70	0.156	1321	0.16	1413	0.972	0.984	98.443	0.168
3.376-3.645	0.161	77	0.16	1172	0.16	1298	0.983	0.983	96.225	0.18
3.645-3.99	0.233	63	0.15	1082	0.154	1214	0.968	0.985	94.3163	0.179
3.99-4.458	0.186	61	0.15	946	0.152	1119	0.976	0.986	89.9911	0.18
4.458-5.14	0.208	42	0.147	878	0.15	1007	0.977	0.987	91.3605	0.184
5.14-6.279	0.186	37	0.175	822	0.176	867	0.981	0.984	99.0773	0.218
6.279-8.81	0.268	40	0.192	650	0.196	695	0.967	0.981	99.2806	0.242
8.81-49.675	0.42	18	0.248	424	0.256	453	0.828	0.949	97.5717	0.358

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