PDB-8ovs: Crystal structure of YeGT glycosyltransferase with bound UDP

ID or keywords:

Entry

Database: PDB / ID: 8ovs

Title

Crystal structure of YeGT glycosyltransferase with bound UDP

Components

YeGT glycosyltransferase

Keywords

TRANSFERASE / Glycosyltransferase / effector protein / nucleotide binding protein

Function / homology

ACETATE ION / : / : / URIDINE-5'-DIPHOSPHATE

Function and homology information

Biological species

Yersinia enterocolitica (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.123 Å

Authors

Wirth, C. / Hunte, C.

Funding support

Germany, 2items

Citation

Journal: J.Biol.Chem. / Year: 2024
Title: Tyrosine-modifying glycosylation by Yersinia effectors.
Authors: Schneider, S. / Wirth, C. / Jank, T. / Hunte, C. / Aktories, K.

History

Deposition	Apr 26, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	May 22, 2024	Provider: repository / Type: Initial release
Revision 1.1	Jun 5, 2024	Group: Database references / Category: citation / Item: _citation.journal_volume

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8ovs.cif.gz	271.2 KB	Display	PDBx/mmCIF format
PDB format	pdb8ovs.ent.gz		Display	PDB format
PDBx/mmJSON format	8ovs.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/ov/8ovs ftp://data.pdbj.org/pub/pdb/validation_reports/ov/8ovs	HTTPS FTP

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Related structure data

Related structure data	8ovtC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&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

AAA: YeGT glycosyltransferase

BBB: YeGT glycosyltransferase

hetero molecules

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

1

AAA: YeGT glycosyltransferase

hetero molecules

defined by author
Evidence: gel filtration, gel filtration experiment suggest YeGT is monomeric in solution
36 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

BBB: YeGT glycosyltransferase

hetero molecules

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

Unit cell

Length a, b, c (Å)	47.130, 114.546, 69.376
Angle α, β, γ (deg.)	90.000, 89.987, 90.000
Int Tables number	4
Space group name H-M	P12₁1

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Protein , 1 types, 2 molecules AAABBB

#1: Protein	YeGT glycosyltransferase Mass: 33958.883 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Yersinia enterocolitica (bacteria) / Strain: Y2wildboar1B / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria)

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Non-polymers , 7 types, 910 molecules

#2: Chemical	ChemComp-UDP / URIDINE-5'-DIPHOSPHATE Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₉H₁₄N₂O₁₂P₂ / Feature type: SUBJECT OF INVESTIGATION / Comment: UDP*YM
#3: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₂H₃O₂
#4: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C₂H₆O₂
#5: Chemical	ChemComp-CD / CADMIUM ION Mass: 112.411 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: Cd
#6: Chemical	ChemComp-MN / MANGANESE (II) ION Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#8: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 871 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.76 Å³/Da / Density % sol: 55.39 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 100mM HEPES pH 7.5, 500mM sodium acetate, 50mM cadmium sulfate

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

ESRF

/ Beamline: ID23-1 / Wavelength: 1 Å

Detector

Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 13, 2017

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection twin

Type	Crystal-ID	ID	Operator	Domain-ID	Fraction
pseudo-merohedral	1	1	H, K, L	1	0.5343
pseudo-merohedral	2	2	-h,-k,l	2	0.4657

Reflection

Resolution: 1.12→47.13 Å / Num. obs: 213705 / % possible obs: 92.7 % / Redundancy: 30.3 % / CC_1/2: 0.999 / R_merge(I) obs: 0.132 / R_pim(I) all: 0.023 / Net I/σ(I): 18

Reflection shell

Resolution: 1.12→1.22 Å / Redundancy: 18.4 % / R_merge(I) obs: 2.038 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 10686 / CC_1/2: 0.39 / R_pim(I) all: 0.479

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
MxCuBE		data collection
autoPROC		data processing
PHASER		phasing
STARANISO		data scaling
Coot		model building
autoPROC		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.123→47.13 Å / Cor.coef. F_o:F_c: 0.978 / Cor.coef. F_o:F_c free: 0.972 / SU B: 0.797 / SU ML: 0.018 / Cross valid method: FREE R-VALUE / ESU R: 0.008 / ESU R Free: 0.007
Details: Hydrogens have been added in their riding positions during refinement. Twin refinement was used with a twin fraction of 0.466 for -h, -k, l as determined by Refmac.

	R_factor	Num. reflection	% reflection
R_free	0.1685	10763	5.037 %
R_work	0.1533	202936	-
all	0.154	-	-
obs	-	213699	76.61 %

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: 17.643 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-8.967 Å²	-0 Å²	-0.612 Å²
2-	-	13.568 Å²	0 Å²
3-	-	-	-4.601 Å²

Refinement step

Cycle: LAST / Resolution: 1.123→47.13 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4369	0	132	871	5372

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.006	0.013	4816
X-RAY DIFFRACTION	r_bond_other_d	0.01	0.016	4560
X-RAY DIFFRACTION	r_angle_refined_deg	1.196	1.654	6401
X-RAY DIFFRACTION	r_angle_other_deg	1.231	1.589	10517
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.678	5	593
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	30.982	23.167	240
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.238	15	843
X-RAY DIFFRACTION	r_dihedral_angle_other_3_deg	18.238	15	4
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.08	15	25
X-RAY DIFFRACTION	r_chiral_restr	0.055	0.2	611
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	5437
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	1095
X-RAY DIFFRACTION	r_nbd_refined	0.184	0.2	975
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.167	0.2	4193
X-RAY DIFFRACTION	r_nbtor_refined	0.159	0.2	2310
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.075	0.2	1918
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.104	0.2	673
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.058	0.2	1
X-RAY DIFFRACTION	r_metal_ion_refined	0.117	0.2	6
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.143	0.2	19
X-RAY DIFFRACTION	r_nbd_other	0.12	0.2	51
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.094	0.2	30
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined	0.058	0.2	1
X-RAY DIFFRACTION	r_mcbond_it	0.832	1.645	2287
X-RAY DIFFRACTION	r_mcbond_other	0.829	1.645	2285
X-RAY DIFFRACTION	r_mcangle_it	1.157	2.472	2878
X-RAY DIFFRACTION	r_mcangle_other	1.156	2.472	2879
X-RAY DIFFRACTION	r_scbond_it	1.036	1.8	2529
X-RAY DIFFRACTION	r_scbond_other	0.96	1.788	2487
X-RAY DIFFRACTION	r_scangle_it	1.146	2.61	3514
X-RAY DIFFRACTION	r_scangle_other	1.146	2.61	3515
X-RAY DIFFRACTION	r_lrange_it	2.748	22.019	5837
X-RAY DIFFRACTION	r_lrange_other	2.046	20.435	5546
X-RAY DIFFRACTION	r_rigid_bond_restr	0.714	3	9376

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 (%)
1.123-1.152	0.705	61	0.79	1238	X-RAY DIFFRACTION	6.3089
1.152-1.184	0.532	143	0.6	2930	X-RAY DIFFRACTION	15.316
1.184-1.218	0.643	325	0.509	5689	X-RAY DIFFRACTION	30.8142
1.218-1.256	0.449	553	0.412	9757	X-RAY DIFFRACTION	54.3432
1.256-1.297	0.314	647	0.297	13038	X-RAY DIFFRACTION	74.6509
1.297-1.342	0.287	805	0.246	15291	X-RAY DIFFRACTION	90.3001
1.342-1.393	0.249	865	0.214	16045	X-RAY DIFFRACTION	98.3368
1.393-1.45	0.196	815	0.179	15566	X-RAY DIFFRACTION	99.4294
1.45-1.514	0.167	829	0.139	15025	X-RAY DIFFRACTION	99.8614
1.514-1.588	0.14	758	0.125	14368	X-RAY DIFFRACTION	99.9537
1.588-1.674	0.147	679	0.129	13754	X-RAY DIFFRACTION	99.9723
1.674-1.775	0.151	681	0.13	12910	X-RAY DIFFRACTION	100.0221
1.775-1.898	0.151	621	0.136	12222	X-RAY DIFFRACTION	99.9844
1.898-2.05	0.157	616	0.139	11348	X-RAY DIFFRACTION	99.9499
2.05-2.245	0.145	570	0.136	10418	X-RAY DIFFRACTION	100.0091
2.245-2.51	0.144	519	0.139	9384	X-RAY DIFFRACTION	99.9899
2.51-2.897	0.155	458	0.147	8355	X-RAY DIFFRACTION	99.9887
2.897-3.547	0.167	344	0.144	7073	X-RAY DIFFRACTION	100.0135
3.547-5.01	0.136	287	0.129	5486	X-RAY DIFFRACTION	99.9827
5.01-47.13	0.173	187	0.16	3039	X-RAY DIFFRACTION	99.9071

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