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

ID or keywords:

Entry

Database: PDB / ID: 24td

Title

Crystal structure of GH30 Streptomyces avermitilis endo-beta-1,6-galactanase

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: 1.9 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	24td.cif.gz	115.3 KB	Display	PDBx/mmCIF format
PDB format	pdb24td.ent.gz	83.1 KB	Display	PDB format
PDBx/mmJSON format	24td.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/24td ftp://data.pdbj.org/pub/pdb/validation_reports/4t/24td	HTTPS FTP

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Related structure data

Related structure data	24teC 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

54.6 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)	50.128, 50.128, 331.431
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-772- HOH
2	1	A-862- HOH

#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: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆H₁₃NO₄S / Comment: pH buffer*YM
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 257 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
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: 1.9→100 Å / Num. obs: 35216 / % possible obs: 100 % / Redundancy: 13.8 % / R_merge(I) obs: 0.144 / Net I/σ(I): 17
Reflection shell	Resolution: 1.9→1.97 Å / R_merge(I) obs: 0.728 / Mean I/σ(I) obs: 4.4 / Num. unique obs: 3426

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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: 1.9→49.564 Å / Cor.coef. F_o:F_c: 0.966 / Cor.coef. F_o:F_c free: 0.957 / SU B: 2.565 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.14 / ESU R Free: 0.122
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1837	1752	5.013 %	RANDOM
R_work	0.1524	33195	-	-
all	0.154	-	-	-
obs	-	34947	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: 21.973 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.005 Å²	0 Å²	-0 Å²
2-	-	0.005 Å²	0 Å²
3-	-	-	-0.009 Å²

Refinement step

Cycle: LAST / Resolution: 1.9→49.564 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3547	0	133	257	3937

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.004	0.012	3772
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	3335
X-RAY DIFFRACTION	r_angle_refined_deg	1.236	1.757	5148
X-RAY DIFFRACTION	r_angle_other_deg	0.475	1.732	7636
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.008	5	465
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	5.664	5	21
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	10.707	10	517
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	15.568	10	159
X-RAY DIFFRACTION	r_chiral_restr	0.064	0.2	571
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	4535
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	931
X-RAY DIFFRACTION	r_nbd_refined	0.199	0.2	723
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.194	0.2	3072
X-RAY DIFFRACTION	r_nbtor_refined	0.178	0.2	1853
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.079	0.2	1834
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.134	0.2	266
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.201	0.2	16
X-RAY DIFFRACTION	r_nbd_other	0.224	0.2	62
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.168	0.2	30
X-RAY DIFFRACTION	r_mcbond_it	1.24	2.182	1863
X-RAY DIFFRACTION	r_mcbond_other	1.234	2.181	1863
X-RAY DIFFRACTION	r_mcangle_it	1.875	3.916	2327
X-RAY DIFFRACTION	r_mcangle_other	1.876	3.918	2328
X-RAY DIFFRACTION	r_scbond_it	2.043	2.496	1909
X-RAY DIFFRACTION	r_scbond_other	2.043	2.497	1910
X-RAY DIFFRACTION	r_scangle_it	2.905	4.477	2821
X-RAY DIFFRACTION	r_scangle_other	2.905	4.478	2822
X-RAY DIFFRACTION	r_lrange_it	4.534	24.573	4339
X-RAY DIFFRACTION	r_lrange_other	4.408	23.36	4287

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
1.9-1.949	0.185	118	0.17	2389	0.17	2507	0.977	0.981	100	0.143
1.949-2.003	0.217	118	0.168	2365	0.171	2484	0.969	0.982	99.9597	0.145
2.003-2.061	0.209	103	0.159	2247	0.161	2350	0.972	0.984	100	0.136
2.061-2.124	0.17	114	0.148	2224	0.149	2338	0.981	0.986	100	0.127
2.124-2.193	0.184	112	0.145	2139	0.147	2252	0.98	0.987	99.9556	0.126
2.193-2.27	0.196	116	0.149	2080	0.151	2198	0.976	0.986	99.909	0.13
2.27-2.356	0.208	130	0.147	1964	0.151	2094	0.973	0.986	100	0.13
2.356-2.452	0.185	108	0.141	1940	0.144	2048	0.98	0.988	100	0.127
2.452-2.56	0.193	104	0.138	1852	0.141	1956	0.98	0.988	100	0.126
2.56-2.685	0.178	105	0.131	1782	0.134	1887	0.981	0.989	100	0.121
2.685-2.83	0.188	97	0.14	1720	0.143	1818	0.977	0.989	99.945	0.136
2.83-3.001	0.206	79	0.138	1616	0.141	1695	0.974	0.988	100	0.14
3.001-3.207	0.226	71	0.151	1560	0.154	1631	0.976	0.985	100	0.155
3.207-3.463	0.152	72	0.138	1432	0.139	1504	0.982	0.988	100	0.151
3.463-3.792	0.151	84	0.137	1326	0.138	1410	0.987	0.988	100	0.154
3.792-4.236	0.153	60	0.14	1235	0.141	1297	0.985	0.988	99.8458	0.161
4.236-4.885	0.2	47	0.152	1101	0.154	1150	0.977	0.986	99.8261	0.184
4.885-5.969	0.199	54	0.188	954	0.189	1008	0.983	0.982	100	0.232
5.969-8.381	0.152	35	0.192	778	0.19	813	0.989	0.981	100	0.234
8.381-49.564	0.205	25	0.229	488	0.228	513	0.974	0.963	100	0.329

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