PDB-8xsh: Crystal structure of the Actinobacillus minor NM305 glucosyltrans...

ID or keywords:

Entry

Database: PDB / ID: 8xsh

Title

Crystal structure of the Actinobacillus minor NM305 glucosyltransferase

Components

Putative glycosyltransferase

Keywords

TRANSFERASE / glycosylation / glycosyltransferase / glucosyltransferase / GT-B fold

Function / homology

: / Glycosyl transferase, family 1 / Glycosyl transferases group 1 / glycosyltransferase activity / Putative glycosyltransferase

Function and homology information

Biological species

Actinobacillus minor NM305 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.85 Å

Authors

Yamasaki, T. / Kohda, D.

Funding support

Japan, 1items

Citation

Journal: J.Biol.Chem. / Year: 2025
Title: An uncharacterized gene from the Actinobacillus genus encodes a glucosyltransferase with successive transfer activity and unique substrate specificity.
Authors: Yamasaki, T. / Kohda, D.

History

Deposition	Jan 9, 2024	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jan 15, 2025	Provider: repository / Type: Initial release
Revision 1.1	Jul 2, 2025	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8xsh.cif.gz	362.9 KB	Display	PDBx/mmCIF format
PDB format	pdb8xsh.ent.gz	223.5 KB	Display	PDB format
PDBx/mmJSON format	8xsh.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	8xsh_validation.pdf.gz	416.1 KB	Display	wwPDB validaton report
Full document	8xsh_full_validation.pdf.gz	416.3 KB	Display
Data in XML	8xsh_validation.xml.gz	17.3 KB	Display
Data in CIF	8xsh_validation.cif.gz	24.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/xs/8xsh ftp://data.pdbj.org/pub/pdb/validation_reports/xs/8xsh	HTTPS FTP

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Related structure data

Related structure data	8xsgC 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	#254 - Feb 2021 Cellulose Synthase similarity (2)

Deposited unit

A: Putative glycosyltransferase

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

1

A: Putative glycosyltransferase

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

Unit cell

Length a, b, c (Å)	93.592, 44.312, 90.754
Angle α, β, γ (deg.)	90.000, 113.745, 90.000
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	A-476- HOH

#1: Protein	Putative glycosyltransferase Mass: 39619.977 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: GLY 1 EXPRESSION TAG PRO 2 EXPRESSION TAG / Source: (gene. exp.) Actinobacillus minor NM305 (bacteria) / Gene: AM305_00150 / Production host: Escherichia coli (E. coli) / References: UniProt: C5RYK2
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 203 / 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	Density Matthews: 2.19 Å³/Da / Density % sol: 43.76 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1 M MES pH 6.5, 0.2 M sodium formate, 14% (w/v) PEG3350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 4, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.85→50 Å / Num. obs: 29001 / % possible obs: 98.9 % / Redundancy: 1.9 % / CC_1/2: 0.998 / R_merge(I) obs: 0.02 / Net I/σ(I): 38.7
Reflection shell	Resolution: 1.85→1.89 Å / R_merge(I) obs: 0.099 / Num. unique obs: 1537 / CC_1/2: 0.885

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0403	refinement
XDS		data reduction
Aimless		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: AlphaFold(AF-B3H2N1-F1)

Resolution: 1.85→46.487 Å / Cor.coef. F_o:F_c: 0.952 / Cor.coef. F_o:F_c free: 0.915 / WR_factor R_free: 0.227 / WR_factor R_work: 0.171 / SU B: 5.967 / SU ML: 0.082 / Average fsc free: 0.9719 / Average fsc work: 0.9867 / Cross valid method: FREE R-VALUE / ESU R: 0.594 / ESU R Free: 0.131
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2111	1425	4.914 %
R_work	0.1563	27575	-
all	0.159	-	-
obs	-	29000	98.787 %

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: 11.551 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.41 Å²	-0 Å²	0.292 Å²
2-	-	-2.078 Å²	-0 Å²
3-	-	-	0.297 Å²

Refinement step

Cycle: LAST / Resolution: 1.85→46.487 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2779	0	0	203	2982

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.012	2848
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	2671
X-RAY DIFFRACTION	r_angle_refined_deg	1.466	1.654	3847
X-RAY DIFFRACTION	r_angle_other_deg	0.5	1.572	6156
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.481	5	338
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	9.279	5	18
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.545	10	502
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	17.081	10	148
X-RAY DIFFRACTION	r_chiral_restr	0.071	0.2	407
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	3331
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	685
X-RAY DIFFRACTION	r_nbd_refined	0.219	0.2	514
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.191	0.2	2414
X-RAY DIFFRACTION	r_nbtor_refined	0.19	0.2	1402
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.08	0.2	1502
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.149	0.2	157
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.022	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.216	0.2	19
X-RAY DIFFRACTION	r_nbd_other	0.21	0.2	79
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.179	0.2	18
X-RAY DIFFRACTION	r_mcbond_it	0.645	1.043	1355
X-RAY DIFFRACTION	r_mcbond_other	0.645	1.042	1355
X-RAY DIFFRACTION	r_mcangle_it	1.026	1.87	1692
X-RAY DIFFRACTION	r_mcangle_other	1.026	1.871	1693
X-RAY DIFFRACTION	r_scbond_it	0.845	1.311	1493
X-RAY DIFFRACTION	r_scbond_other	0.845	1.311	1492
X-RAY DIFFRACTION	r_scangle_it	1.159	2.285	2155
X-RAY DIFFRACTION	r_scangle_other	1.159	2.286	2156
X-RAY DIFFRACTION	r_lrange_it	2.133	12.675	3184
X-RAY DIFFRACTION	r_lrange_other	2.024	12.553	3149
X-RAY DIFFRACTION	r_rigid_bond_restr	3.376	3	5519

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
1.85-1.898	0.233	95	0.134	1768	0.139	2118	0.967	0.991	87.9603	0.121
1.898-1.95	0.241	105	0.154	1952	0.159	2093	0.962	0.987	98.28	0.144
1.95-2.006	0.194	116	0.14	1930	0.143	2048	0.978	0.989	99.9023	0.135
2.006-2.068	0.257	115	0.143	1874	0.149	1989	0.958	0.989	100	0.14
2.068-2.136	0.259	97	0.149	1818	0.154	1915	0.966	0.987	100	0.149
2.136-2.21	0.201	90	0.144	1757	0.147	1849	0.976	0.988	99.8918	0.146
2.21-2.294	0.223	91	0.147	1709	0.151	1804	0.973	0.987	99.7783	0.15
2.294-2.387	0.193	74	0.133	1654	0.136	1731	0.977	0.99	99.8267	0.139
2.387-2.493	0.184	81	0.15	1590	0.152	1674	0.976	0.987	99.8208	0.157
2.493-2.614	0.191	80	0.161	1526	0.163	1610	0.977	0.985	99.7515	0.17
2.614-2.755	0.268	52	0.186	1448	0.189	1502	0.952	0.979	99.8668	0.201
2.755-2.922	0.224	74	0.184	1355	0.186	1433	0.971	0.98	99.7209	0.197
2.922-3.123	0.203	56	0.174	1287	0.176	1348	0.973	0.982	99.6291	0.191
3.123-3.371	0.161	49	0.169	1211	0.168	1266	0.985	0.984	99.5261	0.191
3.371-3.691	0.202	64	0.163	1105	0.166	1174	0.979	0.985	99.5741	0.193
3.691-4.124	0.203	42	0.137	996	0.139	1043	0.98	0.99	99.5206	0.172
4.124-4.756	0.184	47	0.148	899	0.149	954	0.983	0.99	99.1614	0.186
4.756-5.809	0.216	41	0.169	747	0.171	796	0.978	0.989	98.995	0.207
5.809-8.152	0.169	31	0.169	592	0.169	624	0.982	0.985	99.8397	0.209
8.152-46.487	0.259	25	0.175	357	0.18	384	0.962	0.984	99.4792	0.261

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