PDB-7vlb: Crystal structure of UGT109A1 from Bacillus

ID or keywords:

Entry

Database: PDB / ID: 7vlb

Title

Crystal structure of UGT109A1 from Bacillus

Components

UDP-glycosyltransferase

Keywords

TRANSFERASE / glycosyl transferase / UGT109A1

Function / homology

Function and homology information

UDP-glycosyltransferase activity / hexosyltransferase activity / antibiotic biosynthetic process / nucleotide binding
Similarity search - Function

Biological species

Bacillus subtilis subsp. spizizenii (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3 Å

Authors

Chen, L.Q. / Zhang, Y.

Funding support

1items

Citation

Journal: To Be Published
Title: Crystal structure of UGT109A1 from Bacillus
Authors: Chen, L.Q. / Zhang, Y.

History

Deposition	Oct 2, 2021	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Oct 5, 2022	Provider: repository / Type: Initial release
Revision 1.1	Nov 29, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7vlb.cif.gz	275.3 KB	Display	PDBx/mmCIF format
PDB format	pdb7vlb.ent.gz	226.6 KB	Display	PDB format
PDBx/mmJSON format	7vlb.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7vlb_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	7vlb_full_validation.pdf.gz	1.1 MB	Display
Data in XML	7vlb_validation.xml.gz	29.4 KB	Display
Data in CIF	7vlb_validation.cif.gz	39.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/vl/7vlb ftp://data.pdbj.org/pub/pdb/validation_reports/vl/7vlb	HTTPS FTP

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Related structure data

Related structure data	1iirS 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	#156 - Dec 2012 ABO Blood Type Glycosyltransferases similarity (1) #254 - Feb 2021 Cellulose Synthase similarity (1) #141 - Sep 2011 O-GlcNAc Transferase similarity (1)

Deposited unit

A: UDP-glycosyltransferase

B: UDP-glycosyltransferase

hetero molecules

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

1

A: UDP-glycosyltransferase

hetero molecules

defined by author&software
Evidence: gel filtration
44.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: UDP-glycosyltransferase

hetero molecules

defined by author&software
44.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	137.874, 137.874, 135.730
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	96
Space group name H-M	P4₃2₁2

#1: Protein	UDP-glycosyltransferase Mass: 43829.117 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis subsp. spizizenii (bacteria) Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: A0A289QH46
#2: Chemical	ChemComp-UDP / URIDINE-5'-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 Mass: 18.015 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	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: 3.68 Å³/Da / Density % sol: 66.57 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: PEG 3350

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Data collection

Diffraction	Mean temperature: 80 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.989 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 10, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.989 Å / Relative weight: 1
Reflection	Resolution: 3→48.75 Å / Num. obs: 26821 / % possible obs: 100 % / Redundancy: 20 % / CC_1/2: 1 / R_merge(I) obs: 0.078 / R_rim(I) all: 0.08 / Net I/σ(I): 23
Reflection shell	Resolution: 3→3.05 Å / R_merge(I) obs: 0.618 / Num. unique obs: 1302 / CC_1/2: 0.97

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
xia2		data reduction
xia2		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1IIR

1iir

Resolution: 3→48.746 Å / Cor.coef. F_o:F_c: 0.918 / Cor.coef. F_o:F_c free: 0.881 / Cross valid method: FREE R-VALUE / ESU R: 1.189 / ESU R Free: 0.403
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2754	1297	4.845 %
R_work	0.2313	25472	-
all	0.234	-	-
obs	-	26769	99.884 %

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: 87.384 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.464 Å²	-0 Å²	-0 Å²
2-	-	1.464 Å²	-0 Å²
3-	-	-	-2.929 Å²

Refinement step

Cycle: LAST / Resolution: 3→48.746 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5780	0	50	22	5852

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.006	0.013	5937
X-RAY DIFFRACTION	r_bond_other_d	0.035	0.016	5682
X-RAY DIFFRACTION	r_angle_refined_deg	1.728	1.65	8032
X-RAY DIFFRACTION	r_angle_other_deg	2.329	1.581	13156
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.968	5	734
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	39.237	24.618	288
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	19.871	15	1075
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	21.538	15	21
X-RAY DIFFRACTION	r_chiral_restr	0.067	0.2	777
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	6655
X-RAY DIFFRACTION	r_gen_planes_other	0.005	0.02	1239
X-RAY DIFFRACTION	r_nbd_refined	0.227	0.2	1460
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.242	0.2	5882
X-RAY DIFFRACTION	r_nbtor_refined	0.173	0.2	2831
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.074	0.2	2762
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.152	0.2	152
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.01	0.2	4
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.447	0.2	18
X-RAY DIFFRACTION	r_nbd_other	0.197	0.2	22
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.321	0.2	1
X-RAY DIFFRACTION	r_mcbond_it	6.386	9.146	2948
X-RAY DIFFRACTION	r_mcbond_other	6.385	9.144	2947
X-RAY DIFFRACTION	r_mcangle_it	9.829	13.711	3678
X-RAY DIFFRACTION	r_mcangle_other	9.828	13.714	3679
X-RAY DIFFRACTION	r_scbond_it	6.35	9.505	2988
X-RAY DIFFRACTION	r_scbond_other	6.349	9.506	2987
X-RAY DIFFRACTION	r_scangle_it	9.743	14.038	4354
X-RAY DIFFRACTION	r_scangle_other	9.742	14.037	4355
X-RAY DIFFRACTION	r_lrange_it	13.599	108.396	6587
X-RAY DIFFRACTION	r_lrange_other	13.598	108.386	6588

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
3-3.078	0.339	89	0.309	1847	0.311	1936	0.778	0.762	100	0.298
3.078-3.162	0.326	73	0.289	1807	0.29	1881	0.766	0.8	99.9468	0.273
3.162-3.253	0.311	84	0.264	1754	0.266	1838	0.806	0.848	100	0.243
3.253-3.353	0.299	102	0.252	1684	0.255	1786	0.86	0.861	100	0.224
3.353-3.462	0.279	95	0.254	1648	0.256	1743	0.864	0.898	100	0.233
3.462-3.583	0.282	88	0.225	1599	0.228	1687	0.895	0.912	100	0.201
3.583-3.717	0.292	59	0.246	1563	0.247	1622	0.872	0.898	100	0.221
3.717-3.868	0.241	89	0.224	1478	0.225	1567	0.918	0.912	100	0.19
3.868-4.039	0.256	96	0.195	1401	0.199	1503	0.931	0.938	99.6008	0.161
4.039-4.235	0.228	79	0.179	1372	0.182	1452	0.945	0.948	99.9311	0.145
4.235-4.462	0.247	49	0.188	1328	0.19	1377	0.936	0.944	100	0.147
4.462-4.73	0.246	58	0.187	1258	0.189	1316	0.93	0.944	100	0.151
4.73-5.053	0.22	34	0.204	1198	0.204	1232	0.93	0.935	100	0.168
5.053-5.453	0.295	55	0.226	1100	0.229	1155	0.9	0.916	100	0.177
5.453-5.966	0.312	54	0.251	1029	0.254	1083	0.883	0.899	100	0.204
5.966-6.658	0.299	53	0.254	919	0.257	972	0.884	0.905	100	0.214
6.658-7.664	0.25	49	0.228	831	0.229	886	0.913	0.926	99.3228	0.197
7.664-9.329	0.272	47	0.21	701	0.213	756	0.91	0.943	98.9418	0.193
9.329-12.958	0.305	25	0.222	581	0.226	606	0.899	0.935	100	0.215
12.958-48.746	0.372	19	0.439	373	0.436	392	0.853	0.806	100	0.394

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