PDB-8p20: TarM(Se)_G117R-UDP-4RboP-glucose

ID or keywords:

Entry

Database: PDB / ID: 8p20

Title

TarM(Se)_G117R-UDP-4RboP-glucose

Components

TarM(Se)_G117R

Keywords

TRANSFERASE /

Staphylococcus epidermidis / wall teichoic acid glycosyltransferase / GT-B fold / alpha-O-glucose.

Function / homology

Chem-BJT /

BETA-MERCAPTOETHANOL / URIDINE-5'-DIPHOSPHATE

Function and homology information

Biological species

Staphylococcus epidermidis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MIR / Resolution: 2.848 Å

Authors

Guo, Y. / Stehle, T.

Funding support

Germany, 1items

Citation

Journal: Sci Adv / Year: 2023
Title: Invasive Staphylococcus epidermidis uses a unique processive wall teichoic acid glycosyltransferase to evade immune recognition.
Authors: Guo, Y. / Du, X. / Krusche, J. / Beck, C. / Ali, S. / Walter, A. / Winstel, V. / Mayer, C. / Codee, J.D.C. / Peschel, A. / Stehle, T.

History

Deposition	May 14, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Dec 6, 2023	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8p20.cif.gz	415 KB	Display	PDBx/mmCIF format
PDB format	pdb8p20.ent.gz		Display	PDB format
PDBx/mmJSON format	8p20.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/p2/8p20 ftp://data.pdbj.org/pub/pdb/validation_reports/p2/8p20	HTTPS FTP

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Related structure data

Related structure data	7qd7C 7qh9C 7qntC 8p1xC 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) #234 - Jun 2019 MDM2 and Cancer similarity (1) #252 - Dec 2020 Hepatitis C Virus Protease/Helicase similarity (1) #9 - Sep 2000 Lysozyme similarity (1)

Deposited unit

AAA: TarM(Se)_G117R

BBB: TarM(Se)_G117R

CCC: TarM(Se)_G117R

DDD: TarM(Se)_G117R

hetero molecules

246 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

AAA: TarM(Se)_G117R

hetero molecules

defined by author
Evidence: gel filtration
61.4 kDa, 1 polymers

2

BBB: TarM(Se)_G117R

hetero molecules

defined by author
61.4 kDa, 1 polymers

3

CCC: TarM(Se)_G117R

hetero molecules

defined by author
61.5 kDa, 1 polymers

4

DDD: TarM(Se)_G117R

hetero molecules

defined by author
61.4 kDa, 1 polymers

Unit cell

Length a, b, c (Å)	58.620, 75.750, 129.400
Angle α, β, γ (deg.)	90.015, 90.039, 90.031
Int Tables number	1
Space group name H-M	P1

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Protein , 1 types, 4 molecules AAABBBCCCDDD

#1: Protein	TarM(Se)_G117R Mass: 59652.496 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus epidermidis (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria)

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Non-polymers , 6 types, 760 molecules

#2: Chemical	ChemComp-BJT / [(2~{R},3~{S},4~{S})-2-[(2~{S},3~{S},4~{R},5~{R},6~{S})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-3,4-bis(oxidanyl)-5-[oxidanyl-[(2~{R},3~{S},4~{S})-2,3,4-tris(oxidanyl)-5-[oxidanyl-[(2~{R},3~{S},4~{S})-2,3,4,5-tetrakis(oxidanyl)pentoxy]phosphoryl]oxy-pentoxy]phosphoryl]oxy-pentyl] [(2~{S},3~{R},4~{R})-2,3,4-tris(oxidanyl)-5-phosphonooxy-pentyl] hydrogen phosphate Mass: 1036.597 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₆H₅₆O₃₄P₄ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical	ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol Mass: 78.133 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C₂H₆OS
#5: Chemical	ChemComp-UDP / URIDINE-5'-DIPHOSPHATE / Uridine diphosphate Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₉H₁₄N₂O₁₂P₂ / Feature type: SUBJECT OF INVESTIGATION / Comment: UDP*YM
#6: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#7: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 734 / 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: 2.49 Å³/Da / Density % sol: 50.69 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.9 Details: 10% PEG 20 000, 25% PEG MME 550, 0.1 M MES/imidazole, pH 6.9, 0.02 M sodium formate, 0.02 M ammonium acetate, 0.02 M trisodium citrate, 0.02 M sodium potassium tartrate (racemic), 0.02 M sodium oxamate. PH range: 6.2-8.1

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

SLS

/ Beamline: X06DA / Wavelength: 0.99986715688787 Å

Detector

Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 21, 2020

Radiation

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

Radiation wavelength

Wavelength: 0.99986715688787 Å / Relative weight: 1

Reflection twin

Type	Crystal-ID	ID	Operator	Domain-ID	Fraction
pseudo-merohedral	1	1	H, K, L	1	0.414
pseudo-merohedral	2	2	-H, K, -L	2	0.151
pseudo-merohedral	3	3	-h,-k,l	3	0.1626
pseudo-merohedral	4	4	h,-k,-l	4	0.2725

Reflection

Resolution: 2.848→49.23 Å / Num. obs: 51972 / % possible obs: 99.9 % / Redundancy: 4.6 % / CC_1/2: 0.99 / Net I/σ(I): 5.8

Reflection shell

Resolution: 2.848→2.92 Å / Num. unique obs: 3918 / CC_1/2: 0.41 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0258	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MIR / Resolution: 2.848→49.204 Å / Cor.coef. F_o:F_c: 0.91 / Cor.coef. F_o:F_c free: 0.879 / SU B: 9.004 / SU ML: 0.191 / Cross valid method: FREE R-VALUE / ESU R Free: 0.091
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2664	2691	5.178 %
R_work	0.2283	49280	-
all	0.23	-	-
obs	-	51971	99.752 %

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: 48.793 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-13.915 Å²	15.052 Å²	-5.92 Å²
2-	-	55.116 Å²	31.486 Å²
3-	-	-	-41.201 Å²

Refinement step

Cycle: LAST / Resolution: 2.848→49.204 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14004	0	423	734	15161

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.003	0.013	14675
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.018	11482
X-RAY DIFFRACTION	r_angle_refined_deg	1.094	1.676	19988
X-RAY DIFFRACTION	r_angle_other_deg	1.414	1.609	26380
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	3.803	5	1963
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	38.622	24.202	614
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	22.562	15	1880
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	22.021	15	40
X-RAY DIFFRACTION	r_chiral_restr	0.044	0.2	2198
X-RAY DIFFRACTION	r_chiral_restr_other	0.021	0.2	36
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	16956
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	3054
X-RAY DIFFRACTION	r_nbd_refined	0.191	0.2	2095
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.204	0.2	10528
X-RAY DIFFRACTION	r_nbtor_refined	0.171	0.2	7000
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.076	0.2	6856
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.068	0.2	179
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.297	0.2	39
X-RAY DIFFRACTION	r_nbd_other	0.229	0.2	76
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.019	0.2	4
X-RAY DIFFRACTION	r_mcbond_it	1.973	20.02	7864
X-RAY DIFFRACTION	r_mcbond_other	1.972	20.019	7863
X-RAY DIFFRACTION	r_mcangle_it	3.074	27.044	9823
X-RAY DIFFRACTION	r_mcangle_other	3.074	27.045	9824
X-RAY DIFFRACTION	r_scbond_it	1.66	19.679	6811
X-RAY DIFFRACTION	r_scbond_other	1.66	19.68	6810
X-RAY DIFFRACTION	r_scangle_it	2.504	26.583	10165
X-RAY DIFFRACTION	r_scangle_other	2.504	26.583	10166
X-RAY DIFFRACTION	r_lrange_it	5.399	115.374	58632
X-RAY DIFFRACTION	r_lrange_other	5.399	115.372	58633

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 (%)
2.848-2.922	0.388	199	0.297	3604	X-RAY DIFFRACTION	97.8893
2.922-3.002	0.354	190	0.279	3510	X-RAY DIFFRACTION	99.2489
3.002-3.088	0.322	171	0.245	3548	X-RAY DIFFRACTION	100.5135
3.088-3.183	0.306	174	0.248	3293	X-RAY DIFFRACTION	100.0866
3.183-3.287	0.263	192	0.222	3259	X-RAY DIFFRACTION	99.5672
3.287-3.402	0.214	156	0.222	3169	X-RAY DIFFRACTION	99.8199
3.402-3.529	0.261	166	0.234	2952	X-RAY DIFFRACTION	99.9359
3.529-3.673	0.277	182	0.216	3004	X-RAY DIFFRACTION	100.2202
3.673-3.835	0.247	144	0.22	2766	X-RAY DIFFRACTION	99.5893
3.835-4.021	0.307	126	0.213	2649	X-RAY DIFFRACTION	99.892
4.021-4.237	0.234	131	0.204	2573	X-RAY DIFFRACTION	99.8523
4.237-4.492	0.248	170	0.2	2390	X-RAY DIFFRACTION	100.3922
4.492-4.799	0.191	132	0.193	2244	X-RAY DIFFRACTION	99.4558
4.799-5.18	0.255	103	0.211	2119	X-RAY DIFFRACTION	100.1803
5.18-5.668	0.273	132	0.237	1918	X-RAY DIFFRACTION	99.8053
5.668-6.326	0.243	122	0.25	1736	X-RAY DIFFRACTION	100.0538
6.326-7.285	0.237	50	0.259	1611	X-RAY DIFFRACTION	100.1809
7.285-8.874	0.271	61	0.21	1302	X-RAY DIFFRACTION	99.7074
8.874-12.35	0.294	54	0.207	1044	X-RAY DIFFRACTION	100.274
12.35-49.204	0.3	36	0.339	589	X-RAY DIFFRACTION	99.0491

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