PDB-5v4a: A New Glycosyltransferase (DUF1792) from Streptococcus sanguinis

ID or keywords:

Entry

Database: PDB / ID: 5v4a

Title

A New Glycosyltransferase (DUF1792) from Streptococcus sanguinis

Components

GLYCOSYLTRANSFERASE (DUF1792)

Keywords

TRANSFERASE /

Glycosyltransferase / DUF1792

Function / homology

Glycosyltransferase GT-D fold / Glycosyltransferase GT-D fold /

Glycosyl transferase, family 8 / Glycosyl transferase family 8 /

glycosyltransferase activity / Nucleotide-diphospho-sugar transferases / URIDINE-5'-DIPHOSPHATE /

Glycosyltransferase, putative

Function and homology information

Biological species

Streptococcus sanguinis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 1.75 Å

Authors

Zhang, H. / Wu, H.

Citation

Journal: To Be Published
Title: A New Glycosyltransferase (DUF1792) from Streptococcus sanguinis
Authors: Zhang, H. / Wu, H.

History

Deposition	Mar 8, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 13, 2017	Provider: repository / Type: Initial release
Revision 1.1	Nov 22, 2017	Group: Refinement description / Category: software
Revision 1.2	Mar 6, 2024	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5v4a.cif.gz	241 KB	Display	PDBx/mmCIF format
PDB format	pdb5v4a.ent.gz	193.6 KB	Display	PDB format
PDBx/mmJSON format	5v4a.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/v4/5v4a ftp://data.pdbj.org/pub/pdb/validation_reports/v4/5v4a	HTTPS FTP

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Related structure data

Similar structure data	5dj5-d 6ei4-d 3db1-1 5tim-d 4p6s-d 3aio-2 2qy6-1 4p6t-d 7bi7-d 4yrb-1 Search similar-shape structures by Omokage search (details) 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	#156 - Dec 2012 ABO Blood Type Glycosyltransferases similarity (2) #254 - Feb 2021 Cellulose Synthase similarity (2) #141 - Sep 2011 O-GlcNAc Transferase similarity (1)

Deposited unit

A: GLYCOSYLTRANSFERASE (DUF1792)

B: GLYCOSYLTRANSFERASE (DUF1792)

hetero molecules

63.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration, Protein is monomer. The X-ray show show translational NCS present.

Unit cell

Length a, b, c (Å)	42.650, 99.860, 140.120
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P22₁2₁

Components on special symmetry positions

ID	Model	Components
1	1	A-562- HOH
2	1	A-710- HOH

#1: Protein	GLYCOSYLTRANSFERASE (DUF1792) Mass: 31481.525 Da / Num. of mol.: 2 / Fragment: unp residues 801-1074 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus sanguinis (strain SK36) (bacteria) Strain: SK36 / Gene: SSA_0830 / Production host: Escherichia coli (E. coli) / References: UniProt: A3CM53
#2: Chemical	ChemComp-UDP / URIDINE-5'-DIPHOSPHATE / Uridine diphosphate Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₉H₁₄N₂O₁₂P₂ / Comment: UDP*YM
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 643 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.37 Å³/Da / Density % sol: 48.09 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 2M Ammonium Sulfate, 2% PEG 400, 0.1M HEPES pH 7.5

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
Detector	Type: RAYONIX MX300-HS / Detector: CCD / Date: Mar 16, 2012
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.75→42.31 Å / Num. obs: 60928 / % possible obs: 94.25 % / Redundancy: 6 % / Net I/σ(I): 9.7

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Processing

Software

Name	Version	Classification
PHENIX	(1.11.1_2575: ???)	refinement
XDS		data scaling

Refinement

Resolution: 1.75→42.3 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 29.29

	R_factor	Num. reflection	% reflection
R_free	0.2685	1997	3.45 %
R_work	0.2065	-	-
obs	0.2086	57848	94.25 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 1.75→42.3 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4322	0	50	643	5015

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	4466
X-RAY DIFFRACTION	f_angle_d	0.943	6046
X-RAY DIFFRACTION	f_dihedral_angle_d	3.33	2652
X-RAY DIFFRACTION	f_chiral_restr	0.058	654
X-RAY DIFFRACTION	f_plane_restr	0.006	776

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.75-1.7938	0.3865	131	0.2809	3677	X-RAY DIFFRACTION	88
1.7938-1.8422	0.2747	132	0.2567	3680	X-RAY DIFFRACTION	88
1.8422-1.8965	0.3509	134	0.2534	3744	X-RAY DIFFRACTION	90
1.8965-1.9577	0.3532	137	0.253	3797	X-RAY DIFFRACTION	90
1.9577-2.0276	0.2943	142	0.2333	3978	X-RAY DIFFRACTION	95
2.0276-2.1088	0.3177	142	0.2286	3974	X-RAY DIFFRACTION	96
2.1088-2.2048	0.3014	144	0.2138	4027	X-RAY DIFFRACTION	96
2.2048-2.321	0.2893	140	0.2192	3938	X-RAY DIFFRACTION	94
2.321-2.4664	0.2683	146	0.2159	4088	X-RAY DIFFRACTION	97
2.4664-2.6568	0.2741	146	0.2131	4103	X-RAY DIFFRACTION	97
2.6568-2.9242	0.2994	148	0.2091	4124	X-RAY DIFFRACTION	98
2.9242-3.3471	0.2313	150	0.2025	4188	X-RAY DIFFRACTION	98
3.3471-4.2165	0.2226	150	0.1652	4192	X-RAY DIFFRACTION	97
4.2165-42.6627	0.2297	155	0.1838	4341	X-RAY DIFFRACTION	96

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	0.3537	0.0313	0.2024	0.1302	0.0105	0.4205	-0.0074	0.0755	0.0558	-0.0074	0.0089	0.0813	-0.0369	0.0173	-0.0282	0.1727	0.0168	-0.0031	0.1658	0.0274	0.2129	6.1604	29.0344	67.6696
2	1.343	-0.8403	0.0376	0.5793	-0.255	0.9234	0.0822	0.4119	0.356	-0.1828	-0.0774	-0.0367	-0.15	-0.2906	0.0433	0.1659	-0.0072	0.0015	0.296	0.1204	0.1675	8.5552	27.1355	50.1513
3	1.279	0.3766	-0.0567	0.8674	-0.0929	0.8996	0.1092	0.2526	0.2923	-0.0342	-0.0107	0.0842	-0.3065	0.0324	0.0135	0.2407	0.0166	0.0286	0.192	0.0912	0.2739	10.8884	36.8326	63.2952
4	0.4623	0.0567	-0.0952	0.3618	0.1456	0.7277	0.0328	0.0535	0.11	0.0158	0.0091	-0.0046	-0.0639	-0.0027	-0.0007	0.1322	0.0085	-0.0036	0.1395	0.041	0.1516	13.7029	20.6624	71.6823
5	0.7809	0.0572	-0.041	0.715	-0.5997	1.2234	-0.013	0.1898	0.138	-0.2955	0.0294	-0.0369	0.2596	-0.0128	-0.0005	0.1591	-0.0119	0.0036	0.1603	0.0427	0.127	8.8766	9.9319	55.6759
6	0.7442	-0.5023	0.1833	0.6316	-0.3034	0.9725	-0.0845	0.3075	0.1239	-0.1267	0.1493	0.1332	0.0564	-0.1431	-0.0035	0.1416	0.0084	-0.0007	0.1761	0.0587	0.1498	3.8451	15.3035	61.2602
7	0.5276	-0.1262	0.0387	0.1433	0.0735	0.9075	-0.014	0.091	0.0812	-0.0427	0.0264	-0.0197	-0.1063	0.2174	-0.0006	0.1628	-0.0202	0.0009	0.2083	0.0401	0.1698	21.9886	20.1849	65.8844
8	1.0919	1.0242	-0.92	1.2526	-0.8312	0.7773	-0.0575	0.0491	-0.2198	-0.0233	-0.1449	-0.2855	0.0589	0.5908	0.0288	0.1674	-0.0063	0.0076	0.2989	0.0492	0.1829	21.9921	5.226	61.3462
9	0.6415	0.0078	-0.3649	0.4661	-0.0113	2.0448	-0.035	-0.0359	0.1535	0.0528	-0.0474	-0.0008	-0.1316	0.0954	-0.0264	0.1539	-0.0201	-0.0183	0.1731	-0.0481	0.1995	15.0222	28.0449	98.4007
10	2.4061	1.0046	-0.461	0.4478	-0.1483	0.949	0.081	-0.5402	-0.1899	0.1452	-0.1604	-0.0344	0.0055	-0.0091	-0.0442	0.1737	-0.0159	-0.0148	0.261	-0.0894	0.1847	12.5543	24.5288	115.429
11	1.2259	-0.667	-0.1632	0.5516	0.0309	0.8101	-0.114	-0.2951	0.3221	0.05	0.1253	0.0025	-0.2789	0.0648	0.0047	0.2557	0.0044	-0.03	0.2535	-0.0828	0.3175	10.2393	35.29	102.9187
12	1.9248	0.5403	0.27	0.9968	-0.0409	1.3326	-0.002	-0.1921	0.259	0.0408	0.0266	-0.0491	-0.0635	-0.1018	0.0716	0.1509	0.0057	0.015	0.1428	-0.0793	0.2316	8.8547	30.6802	96.3958
13	0.5913	-0.0375	0.1256	0.3542	-0.001	0.6568	0.0272	-0.0491	0.0727	0.0118	0.0142	0	0.0643	0.0186	-0.0031	0.1552	0.0027	0.0016	0.1981	-0.0672	0.1463	10.157	13.1188	99.1419
14	0.7689	-0.7604	-0.0842	0.7869	0.1076	0.7222	0.0099	-0.067	0.1316	-0.0602	0.0305	-0.0668	0.0674	-0.2285	0.0188	0.195	-0.0268	-0.0004	0.2481	-0.054	0.2076	-3.6936	11.6525	102.7791

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 5 through 36 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 37 through 59 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 60 through 103 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 104 through 164 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 165 through 190 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 191 through 214 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 215 through 253 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 254 through 272 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 5 through 37 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 38 through 59 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 60 through 103 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 104 through 124 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 125 through 233 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 234 through 272 )

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