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

ID or keywords:

Entry

Database: PDB / ID: 8xsg

Title

Crystal structure of the Actinobacillus minor NM305 glucosyltransferase in complex with UDP

Components

Putative glycosyltransferase

Keywords

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

Function / homology

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

Function and homology information

Biological species

Actinobacillus minor NM305 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.8 Å

Authors

Yamasaki, T. / Kohda, D.

Funding support

Japan, 1items

Citation

Journal: To Be Published
Title: Crystal structure of the Actinobacillus minor NM305 glucosyltransferase in complex with UDP
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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8xsg.cif.gz	381.1 KB	Display	PDBx/mmCIF format
PDB format	pdb8xsg.ent.gz	236.5 KB	Display	PDB format
PDBx/mmJSON format	8xsg.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/xs/8xsg ftp://data.pdbj.org/pub/pdb/validation_reports/xs/8xsg	HTTPS FTP

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Related structure data

Related structure data	8xshS S: Starting model for refinement
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

hetero molecules

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

1

A: Putative glycosyltransferase

hetero molecules

A: Putative glycosyltransferase

hetero molecules

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

Unit cell

Length a, b, c (Å)	100.136, 43.390, 95.823
Angle α, β, γ (deg.)	90.000, 117.440, 90.000
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	A-590- HOH

#1: Protein	Putative glycosyltransferase Mass: 39619.977 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: GLY A 1 EXPRESSION TAG PRO A 2 EXPRESSION TAG / Source: (gene. exp.) Actinobacillus minor NM305 (bacteria) / Gene: AM305_00150 / Production host: Escherichia coli (E. coli) / References: UniProt: C5RYK2
#2: Chemical	ChemComp-URI / URIDINE Mass: 244.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₉H₁₂N₂O₆ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID Mass: 195.237 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C₆H₁₃NO₄S / Comment: pH buffer*YM
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 215 / Source method: isolated from a natural source / Formula: H₂O
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: 2.33 Å³/Da / Density % sol: 47.24 %
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) PEG 3350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00003 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 29, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.00003 Å / Relative weight: 1
Reflection	Resolution: 1.8→50 Å / Num. obs: 32975 / % possible obs: 96.7 % / Redundancy: 7 % / CC_1/2: 1 / R_merge(I) obs: 0.034 / Net I/σ(I): 33
Reflection shell	Resolution: 1.8→1.84 Å / Num. unique obs: 1948 / CC_1/2: 0.989

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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: 8XSH

8xsh

Resolution: 1.8→42.557 Å / Cor.coef. F_o:F_c: 0.968 / Cor.coef. F_o:F_c free: 0.953 / WR_factor R_free: 0.205 / WR_factor R_work: 0.161 / SU B: 5.731 / SU ML: 0.08 / Average fsc free: 0.9743 / Average fsc work: 0.9869 / Cross valid method: FREE R-VALUE / ESU R: 0.259 / ESU R Free: 0.116
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2013	1696	5.143 %
R_work	0.1584	31278	-
all	0.161	-	-
obs	-	32974	96.339 %

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: 28.179 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.838 Å²	0 Å²	-0.585 Å²
2-	-	-0.417 Å²	-0 Å²
3-	-	-	0.121 Å²

Refinement step

Cycle: LAST / Resolution: 1.8→42.557 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2796	0	29	215	3040

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.012	2896
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	2707
X-RAY DIFFRACTION	r_angle_refined_deg	1.448	1.654	3914
X-RAY DIFFRACTION	r_angle_other_deg	0.515	1.573	6247
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.804	5	341
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	9.498	5	18
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.248	10	503
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	17.207	10	148
X-RAY DIFFRACTION	r_chiral_restr	0.074	0.2	415
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	3362
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	690
X-RAY DIFFRACTION	r_nbd_refined	0.217	0.2	522
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.195	0.2	2447
X-RAY DIFFRACTION	r_nbtor_refined	0.187	0.2	1412
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.08	0.2	1475
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.142	0.2	174
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.06	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.186	0.2	12
X-RAY DIFFRACTION	r_nbd_other	0.142	0.2	69
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.106	0.2	17
X-RAY DIFFRACTION	r_mcbond_it	2.055	2.793	1367
X-RAY DIFFRACTION	r_mcbond_other	2.046	2.793	1367
X-RAY DIFFRACTION	r_mcangle_it	2.837	5.022	1707
X-RAY DIFFRACTION	r_mcangle_other	2.842	5.024	1708
X-RAY DIFFRACTION	r_scbond_it	2.317	3.161	1529
X-RAY DIFFRACTION	r_scbond_other	2.315	3.161	1527
X-RAY DIFFRACTION	r_scangle_it	3.21	5.65	2207
X-RAY DIFFRACTION	r_scangle_other	3.21	5.649	2208
X-RAY DIFFRACTION	r_lrange_it	4.11	28.05	3234
X-RAY DIFFRACTION	r_lrange_other	4.019	27.941	3200
X-RAY DIFFRACTION	r_rigid_bond_restr	3.981	3	5603

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
1.8-1.847	0.231	112	0.184	2294	0.187	2504	0.976	0.986	96.0863	0.168
1.847-1.897	0.251	108	0.173	2090	0.176	2444	0.96	0.987	89.9345	0.154
1.897-1.952	0.212	110	0.155	2118	0.158	2414	0.973	0.986	92.2949	0.135
1.952-2.012	0.213	115	0.136	2110	0.14	2282	0.972	0.989	97.5022	0.123
2.012-2.078	0.198	116	0.142	2069	0.145	2230	0.974	0.988	97.9821	0.128
2.078-2.151	0.204	122	0.145	2012	0.148	2176	0.975	0.988	98.0699	0.133
2.151-2.232	0.198	122	0.139	1921	0.143	2084	0.979	0.989	98.0326	0.13
2.232-2.322	0.203	106	0.144	1857	0.148	2001	0.973	0.988	98.101	0.136
2.322-2.425	0.185	106	0.129	1811	0.132	1952	0.979	0.991	98.207	0.124
2.425-2.543	0.186	99	0.143	1735	0.145	1865	0.978	0.989	98.3378	0.139
2.543-2.68	0.238	79	0.152	1640	0.156	1752	0.972	0.987	98.1164	0.15
2.68-2.842	0.227	85	0.167	1576	0.171	1688	0.967	0.983	98.4005	0.167
2.842-3.038	0.237	72	0.174	1459	0.177	1572	0.965	0.982	97.3919	0.178
3.038-3.28	0.196	60	0.172	1342	0.173	1461	0.978	0.983	95.9617	0.178
3.28-3.59	0.207	56	0.18	1095	0.181	1369	0.976	0.985	84.076	0.19
3.59-4.011	0.186	57	0.159	1148	0.16	1223	0.98	0.987	98.5282	0.173
4.011-4.624	0.195	64	0.142	1029	0.145	1099	0.983	0.989	99.454	0.163
4.624-5.647	0.168	33	0.157	891	0.158	926	0.983	0.989	99.784	0.181
5.647-7.917	0.208	44	0.171	701	0.174	745	0.974	0.985	100	0.189
7.917-42.557	0.16	30	0.204	380	0.201	437	0.986	0.978	93.8215	0.239

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